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Trueba G, Cardenas P, Romo G, Gutierrez B. Reevaluating human-microbiota symbiosis: Strain-level insights and evolutionary perspectives across animal species. Biosystems 2024; 244:105283. [PMID: 39103138 DOI: 10.1016/j.biosystems.2024.105283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 08/01/2024] [Accepted: 08/02/2024] [Indexed: 08/07/2024]
Abstract
The prevailing consensus in scientific literature underscores the mutualistic bond between the microbiota and the human host, suggesting a finely tuned coevolutionary partnership that enhances the fitness of both parties. This symbiotic relationship has been extensively studied, with certain bacterial attributes being construed as hallmarks of natural selection favoring the benefit of the human host. Some scholars go as far as equating the intricate interplay between humans and their intestinal microbiota to that of endosymbiotic relationships, even conceptualizing microbiota as an integral human organ. However, amidst the prevailing narrative of bacterial species being categorized as beneficial or detrimental to human health, a critical oversight often emerges - the inherent functional diversity within bacterial strains. Such reductionist perspectives risk oversimplifying the complex dynamics at play within the microbiome. Recent genomic analysis at the strain level is highly limited, which is surprising given that strain information provides critical data about selective pressures in the intestine. These pressures appear to focus more on the well-being of bacteria rather than human health. Connected to this is the extent to which animals depend on metabolic activity from intestinal bacteria, which varies widely across species. While omnivores like humans exhibit lower dependency, certain herbivores rely entirely on bacterial activity and have developed specialized compartments to house these bacteria.
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Affiliation(s)
- Gabriel Trueba
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador.
| | - Paul Cardenas
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - German Romo
- Escuela de Medicina Veterinaria, Universidad San Francisco de Quito, Quito, Ecuador
| | - Bernardo Gutierrez
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador; Department of Biology, University of Oxford, Oxford, OX1 3SZ, UK
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2
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Diallo A, Overman G, Sah P, Liechti GW. Recognition of Chlamydia trachomatis by Toll-like receptor 9 is altered during persistence. Infect Immun 2024; 92:e0006324. [PMID: 38899879 PMCID: PMC11238561 DOI: 10.1128/iai.00063-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
Toll-like receptor 9 (TLR9) is an innate immune receptor that localizes to endosomes in antigen presenting cells and recognizes single stranded unmethylated CpG sites on bacterial genomic DNA (gDNA). Previous bioinformatic studies have demonstrated that the genome of the human pathogen Chlamydia trachomatis contains TLR9 stimulatory motifs, and correlative studies have implied a link between human TLR9 (hTLR9) genotype variants and susceptibility to infection. Here, we present our evaluation of the stimulatory potential of C. trachomatis gDNA and its recognition by hTLR9- and murine TLR9 (mTLR9)-expressing cells. Utilizing reporter cell lines, we demonstrate that purified gDNA from C. trachomatis can stimulate hTLR9 signaling, albeit at lower levels than gDNA prepared from other Gram-negative bacteria. Interestingly, we found that while C. trachomatis is capable of signaling through hTLR9 and mTLR9 during live infections in HEK293 reporter cell lines, signaling only occurs at later developmental time points. Chlamydia-specific induction of hTLR9 is blocked when protein synthesis is inhibited prior to the RB-to-EB conversion, exacerbated by the inhibition of lipooligosaccharide biosynthesis, and is significantly altered during the induction of aberrance/persistence. Our observations support the hypothesis that chlamydial gDNA is released during the conversion between the pathogen's replicative and infectious forms and during treatment with antibiotics targeting peptidoglycan assembly. Given that C. trachomatis inclusions do not co-localize with TLR9-containing vacuoles in the pro-monocytic cell line U937, our findings also hint that chlamydial gDNA is capable of egress from the inclusion, and traffics to TLR9-containing vacuoles via an as yet unknown pathway.
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Affiliation(s)
- Aissata Diallo
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, Maryland, USA
- Henry Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Grace Overman
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, Maryland, USA
- Henry Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Prakash Sah
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, Maryland, USA
- Henry Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - George W Liechti
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, Maryland, USA
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3
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Osman R, Dema E, David A, Hughes G, Field N, Cole M, Didelot X, Saunders J. Understanding the potential role of whole genome sequencing (WGS) in managing patients with gonorrhoea: A systematic review of WGS use on human pathogens in individual patient care. J Infect 2024; 88:106168. [PMID: 38670270 DOI: 10.1016/j.jinf.2024.106168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 04/19/2024] [Accepted: 04/20/2024] [Indexed: 04/28/2024]
Abstract
OBJECTIVES The utility of whole genome sequencing (WGS) to inform sexually transmitted infection (STI) patient management is unclear. Timely WGS data might support clinical management of STIs by characterising epidemiological links and antimicrobial resistance profiles. We conducted a systematic review of clinical application of WGS to any human pathogen that may be transposable to gonorrhoea. METHODS We searched six databases for articles published between 01/01/2010-06/02/2023 that reported on real/near real-time human pathogen WGS to inform clinical intervention. All article types from all settings were included. Findings were analysed using narrative synthesis. RESULTS We identified 12,179 articles, of which eight reported applications to inform tuberculosis (n = 7) and gonorrhoea (n = 1) clinical patient management. WGS data were successfully used as an adjunct to clinical and epidemiological data to enhance contact-tracing (n = 2), inform antimicrobial therapy (n = 5) and identify cross-contamination (n = 1). WGS identified gonorrhoea transmission chains that were not established via partner notification. Future applications could include insights into pathogen exposure detected within sexual networks for targeted patient management. CONCLUSIONS While there was some evidence of WGS use to provide individualised tuberculosis and gonorrhoea treatment, the eight identified studies contained few participants. Future research should focus on testing WGS intervention effectiveness and examining ethical considerations of STI WGS use.
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Affiliation(s)
- Roeann Osman
- Institute for Global Health, University College London (UCL), Mortimer Market Centre, London WC1E 6JB, United Kingdom; National Institute for Health Research (NIHR) Health Protection Research Unit (HPRU) in Blood Borne and Sexually Transmitted Infections at University College London (UCL), London, United Kingdom.
| | - Emily Dema
- Institute for Global Health, University College London (UCL), Mortimer Market Centre, London WC1E 6JB, United Kingdom
| | - Alexandra David
- Institute for Global Health, University College London (UCL), Mortimer Market Centre, London WC1E 6JB, United Kingdom
| | - Gwenda Hughes
- Department of Infectious Disease Epidemiology and Dynamics, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Nigel Field
- Institute for Global Health, University College London (UCL), Mortimer Market Centre, London WC1E 6JB, United Kingdom
| | - Michelle Cole
- UK Health Security Agency (UK HSA), 61 Colindale Avenue, London NW9 5EQ, United Kingdom
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry CV4 7AL, United Kingdom; National Institute for Health Research (NIHR) Health Protection Research Unit (HPRU) in Genomics and Enabling Data at Warwick University, United Kingdom
| | - John Saunders
- Institute for Global Health, University College London (UCL), Mortimer Market Centre, London WC1E 6JB, United Kingdom; National Institute for Health Research (NIHR) Health Protection Research Unit (HPRU) in Blood Borne and Sexually Transmitted Infections at University College London (UCL), London, United Kingdom; UK Health Security Agency (UK HSA), 61 Colindale Avenue, London NW9 5EQ, United Kingdom
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4
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Potter AD, Criss AK. Dinner date: Neisseria gonorrhoeae central carbon metabolism and pathogenesis. Emerg Top Life Sci 2024; 8:15-28. [PMID: 37144661 PMCID: PMC10625648 DOI: 10.1042/etls20220111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/10/2023] [Accepted: 04/14/2023] [Indexed: 05/06/2023]
Abstract
Neisseria gonorrhoeae, the causative agent of the sexually transmitted infection gonorrhea, is a human-adapted pathogen that does not productively infect other organisms. The ongoing relationship between N. gonorrhoeae and the human host is facilitated by the exchange of nutrient resources that allow for N. gonorrhoeae growth in the human genital tract. What N. gonorrhoeae 'eats' and the pathways used to consume these nutrients have been a topic of investigation over the last 50 years. More recent investigations are uncovering the impact of N. gonorrhoeae metabolism on infection and inflammatory responses, the environmental influences driving N. gonorrhoeae metabolism, and the metabolic adaptations enabling antimicrobial resistance. This mini-review is an introduction to the field of N. gonorrhoeae central carbon metabolism in the context of pathogenesis. It summarizes the foundational work used to characterize N. gonorrhoeae central metabolic pathways and the effects of these pathways on disease outcomes, and highlights some of the most recent advances and themes under current investigation. This review ends with a brief description of the current outlook and technologies under development to increase understanding of how the pathogenic potential of N. gonorrhoeae is enabled by metabolic adaptation.
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Affiliation(s)
- Aimee D. Potter
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA USA
| | - Alison K. Criss
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA USA
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5
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Diallo A, Overman G, Sah P, Liechti GW. Recognition of Chlamydia trachomatis by Toll-Like Receptor 9 is altered during persistence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579186. [PMID: 38370826 PMCID: PMC10871208 DOI: 10.1101/2024.02.06.579186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Toll-like receptor 9 (TLR9) is an innate immune receptor that localizes to endosomes in antigen presenting cells and recognizes single stranded unmethylated CpG sites on bacterial genomic DNA. Previous bioinformatic studies have indicated that the genome of the human pathogen Chlamydia trachomatis contains TLR9 stimulatory motifs, and correlative studies have implied a link between human TLR9 (hTLR9) genotype variants and susceptibility to infection. Here we present our evaluation of the stimulatory potential of C. trachomatis gDNA and its recognition by hTLR9- and murine TLR9 (mTLR9)-expressing cells. We confirm that hTLR9 colocalizes with chlamydial inclusions in the pro-monocytic cell line, U937. Utilizing HEK293 reporter cell lines, we demonstrate that purified genomic DNA from C. trachomatis can stimulate hTLR9 signaling, albeit at lower levels than gDNA prepared from other Gram-negative bacteria. Interestingly, we found that while C. trachomatis is capable of signaling through hTLR9 and mTLR9 during live infections in non-phagocytic HEK293 reporter cell lines, signaling only occurs at later developmental time points. Chlamydia-specific induction of hTLR9 is blocked when protein synthesis is inhibited prior to the RB-to-EB conversion and exacerbated by the inhibition of lipooligosaccharide biosynthesis. The induction of aberrance / persistence also significantly alters Chlamydia-specific TLR9 signaling. Our observations support the hypothesis that chlamydial gDNA is released at appreciable levels by the bacterium during the conversion between its replicative and infectious forms and during treatment with antibiotics targeting peptidoglycan assembly.
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Affiliation(s)
- Aissata Diallo
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD, United States of America
- Henry Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Grace Overman
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD, United States of America
- Henry Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Prakash Sah
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD, United States of America
- Henry Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - George W. Liechti
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD, United States of America
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Raccagni AR, Ranzenigo M, Bruzzesi E, Maci C, Castagna A, Nozza S. Neisseria gonorrhoeae Antimicrobial Resistance: The Future of Antibiotic Therapy. J Clin Med 2023; 12:7767. [PMID: 38137836 PMCID: PMC10744250 DOI: 10.3390/jcm12247767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/25/2023] [Accepted: 12/17/2023] [Indexed: 12/24/2023] Open
Abstract
The growing threat of antibiotic-resistant Neisseria gonorrhoeae, which causes gonorrhea, presents a current public health challenge. Over the years, the pathogen has developed resistance to different antibiotics, leaving few effective treatment options. High-level resistance to key drugs, including ceftriaxone, has become a concerning reality. This article primarily focuses on the treatment of gonorrhea and the current clinical trials aimed at providing new antibiotic treatment options. We explore ongoing efforts to assess new antibiotics, including zoliflodacin, and gepotidacin. These drugs offer new effective treatment options, but their rapid availability remains uncertain. We delve into two ongoing clinical trials: one evaluating the efficacy and safety of gepotidacin compared to the standard ceftriaxone-azithromycin combination and the other assessing the non-inferiority of zoliflodacin versus the combination therapy of ceftriaxone-azithromycin. These trials represent crucial steps in the search for alternative treatments for uncomplicated gonorrhea. Notably, gonorrhea has been included in the "WHO Priority Pathogens List for Research and Development of New Antibiotics". In conclusion, the urgent need for innovative treatment strategies is underscored by the rising threat of antibiotic resistance in N. gonorrhoeae; collaboration among researchers, industries, and healthcare authorities is therefore essential.
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Affiliation(s)
- Angelo Roberto Raccagni
- Infectious Diseases Unit, Vita-Salute San Raffaele University, 20132 Milan, Italy; (M.R.); (E.B.); (C.M.); (A.C.); (S.N.)
| | - Martina Ranzenigo
- Infectious Diseases Unit, Vita-Salute San Raffaele University, 20132 Milan, Italy; (M.R.); (E.B.); (C.M.); (A.C.); (S.N.)
| | - Elena Bruzzesi
- Infectious Diseases Unit, Vita-Salute San Raffaele University, 20132 Milan, Italy; (M.R.); (E.B.); (C.M.); (A.C.); (S.N.)
| | - Chiara Maci
- Infectious Diseases Unit, Vita-Salute San Raffaele University, 20132 Milan, Italy; (M.R.); (E.B.); (C.M.); (A.C.); (S.N.)
| | - Antonella Castagna
- Infectious Diseases Unit, Vita-Salute San Raffaele University, 20132 Milan, Italy; (M.R.); (E.B.); (C.M.); (A.C.); (S.N.)
- Infectious Diseases Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Silvia Nozza
- Infectious Diseases Unit, Vita-Salute San Raffaele University, 20132 Milan, Italy; (M.R.); (E.B.); (C.M.); (A.C.); (S.N.)
- Infectious Diseases Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
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7
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Kant R, Jha P, Saluja D, Chopra M. Identification of novel inhibitors of Neisseria gonorrhoeae MurI using homology modeling, structure-based pharmacophore, molecular docking, and molecular dynamics simulation-based approach. J Biomol Struct Dyn 2023; 41:7433-7446. [PMID: 36106953 DOI: 10.1080/07391102.2022.2121943] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 09/01/2022] [Indexed: 10/14/2022]
Abstract
MurI is one of the most significant role players in the biosynthesis of the peptidoglycan layer in Neisseria gonorrhoeae (Ng). We attempted to highlight the structural and functional relationship between Ng-MurI and D-glutamate to design novel molecules targeting this interaction. The three-dimensional (3D) model of the protein was constructed by homology modeling and the quality and consistency of generated model were assessed. The binding site of the protein was identified by molecular docking studies and a pharmacophore was identified using the interactions of the control ligand. The structure-based pharmacophore model was validated and employed for high-throughput virtual screening and molecular docking to identify novel Ng-MurI inhibitors. Finally, the model was optimized by molecular dynamics (MD) simulations and the optimized model complex with the substrate glutamate and novel molecules facilitated us to confirm the stability of the protein-ligand docked complexes. The 100 ns MD simulations of the potential lead compounds with protein confirmed that the modeled complexes were stable. This study identifies novel potential compounds with good fitness and docking scores, which made the interactions of biological significance within the protein active site. Hence, the identified compounds may act as new leads to design and develop Ng-MurI inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ravi Kant
- Medical Biotechnology Laboratory, Dr. B. R. Ambedkar Center for Biomedical Research & Delhi School of Public Health, IoE, University of Delhi, Delhi, India
| | - Prakash Jha
- Laboratory of Molecular Modeling and Drug Development, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Daman Saluja
- Medical Biotechnology Laboratory, Dr. B. R. Ambedkar Center for Biomedical Research & Delhi School of Public Health, IoE, University of Delhi, Delhi, India
| | - Madhu Chopra
- Laboratory of Molecular Modeling and Drug Development, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
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8
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Ryan ME, Damke PP, Shaffer CL. DNA Transport through the Dynamic Type IV Secretion System. Infect Immun 2023; 91:e0043622. [PMID: 37338415 PMCID: PMC10353360 DOI: 10.1128/iai.00436-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023] Open
Abstract
The versatile type IV secretion system (T4SS) nanomachine plays a pivotal role in bacterial pathogenesis and the propagation of antibiotic resistance determinants throughout microbial populations. In addition to paradigmatic DNA conjugation machineries, diverse T4SSs enable the delivery of multifarious effector proteins to target prokaryotic and eukaryotic cells, mediate DNA export and uptake from the extracellular milieu, and in rare examples, facilitate transkingdom DNA translocation. Recent advances have identified new mechanisms underlying unilateral nucleic acid transport through the T4SS apparatus, highlighting both functional plasticity and evolutionary adaptations that enable novel capabilities. In this review, we describe the molecular mechanisms underscoring DNA translocation through diverse T4SS machineries, emphasizing the architectural features that implement DNA exchange across the bacterial membrane and license transverse DNA release across kingdom boundaries. We further detail how recent studies have addressed outstanding questions surrounding the mechanisms by which nanomachine architectures and substrate recruitment strategies contribute to T4SS functional diversity.
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Affiliation(s)
- Mackenzie E. Ryan
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Prashant P. Damke
- Department of Veterinary Sciences, University of Kentucky College of Agriculture, Lexington, Kentucky, USA
| | - Carrie L. Shaffer
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky College of Medicine, Lexington, Kentucky, USA
- Department of Veterinary Sciences, University of Kentucky College of Agriculture, Lexington, Kentucky, USA
- Department of Pharmaceutical Sciences, University of Kentucky College of Pharmacy, Lexington, Kentucky, USA
- Markey Cancer Center, University of Kentucky College of Medicine, Lexington, Kentucky, USA
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9
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Seow VY, Tsygelnytska O, Biais N. Multisite transformation in Neisseria gonorrhoeae: insights on transformations mechanisms and new genetic modification protocols. Front Microbiol 2023; 14:1178128. [PMID: 37408636 PMCID: PMC10319059 DOI: 10.3389/fmicb.2023.1178128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/31/2023] [Indexed: 07/07/2023] Open
Abstract
Natural transformation, or the uptake of naked DNA from the external milieu by bacteria, holds a unique place in the history of biology. This is both the beginning of the realization of the correct chemical nature of genes and the first technical step to the molecular biology revolution that sees us today able to modify genomes almost at will. Yet the mechanistic understanding of bacterial transformation still presents many blind spots and many bacterial systems lag behind power horse model systems like Escherichia coli in terms of ease of genetic modification. Using Neisseria gonorrhoeae as a model system and using transformation with multiple DNA molecules, we tackle in this paper both some aspects of the mechanistic nature of bacterial transformation and the presentation of new molecular biology techniques for this organism. We show that similarly to what has been demonstrated in other naturally competent bacteria, Neisseria gonorrhoeae can incorporate, at the same time, different DNA molecules modifying DNA at different loci within its genome. In particular, co-transformation of a DNA molecule bearing an antibiotic selection cassette and another non-selected DNA piece can lead to the integration of both molecules in the genome while selecting only through the selective cassette at percentages above 70%. We also show that successive selections with two selection markers at the same genetic locus can drastically reduce the number of genetic markers needed to do multisite genetic modifications in Neisseria gonorrhoeae. Despite public health interest heightened with the recent rise in antibiotic resistance, the causative agent of gonorrhea still does not possess a plethora of molecular techniques. This paper will extend the techniques available to the Neisseria community while providing some insights into the mechanisms behind bacterial transformation in Neisseria gonorrhoeae. We are providing a suite of new techniques to quickly obtain modifications of genes and genomes in the Neisserial naturally competent bacteria.
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Affiliation(s)
- Vui Yin Seow
- Brooklyn College of the City University of New York, Brooklyn, NY, United States
- The Graduate Center of the City University of New York, New York, NY, United States
- Laboratoire Jean Perrin, UMR8237, Sorbonne Université, Paris, France
| | - Olga Tsygelnytska
- Brooklyn College of the City University of New York, Brooklyn, NY, United States
| | - Nicolas Biais
- Brooklyn College of the City University of New York, Brooklyn, NY, United States
- The Graduate Center of the City University of New York, New York, NY, United States
- Laboratoire Jean Perrin, UMR8237, Sorbonne Université, Paris, France
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10
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Kravtsov D, Gryadunov D, Shaskolskiy B. Gonococcal Genetic Island in the Global Neisseria gonorrhoeae Population: A Model of Genetic Diversity and Association with Resistance to Antimicrobials. Microorganisms 2023; 11:1547. [PMID: 37375049 DOI: 10.3390/microorganisms11061547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
The aim of this work was to study the genetic diversity of the gonococcal genetic island (GGI) responsible for the type IV secretion system (T4SS) and the association of a functionally active GGI with antimicrobial resistance. An analysis of the GGI in a sample of 14,763 genomes of N. gonorrhoeae isolates from the Pathogenwatch database collected in 1996-2019 from 68 countries was performed. A model of GGI's genetic diversity that divides the global gonococcal population into fifty-one GGI clusters and three GGI superclusters based on the allele type of the traG gene and substitutions of the atlA and ych genes for eppA and ych1 has been proposed, reflecting differences among isolates in the T4SS functionality. The NG-MAST and MLST typing schemes (with accuracies of 91% and 83%, respectively) allowed the determination of both the presence of a GGI and the GGI cluster and, correspondingly, the structure of the GGI and the ability to secrete DNA. A statistically significant difference in the proportion of N. gonorrhoeae isolates resistant to ciprofloxacin, cefixime, tetracycline, and penicillin was found when comparing populations with a functional and a non-functional GGI. The presence of a functional GGI did not affect the proportion of azithromycin-resistant isolates.
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Affiliation(s)
- Dmitry Kravtsov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Dmitry Gryadunov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Boris Shaskolskiy
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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11
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Moura de Sousa J, Lourenço M, Gordo I. Horizontal gene transfer among host-associated microbes. Cell Host Microbe 2023; 31:513-527. [PMID: 37054673 DOI: 10.1016/j.chom.2023.03.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
Horizontal gene transfer is an important evolutionary force, facilitating bacterial diversity. It is thought to be pervasive in host-associated microbiomes, where bacterial densities are high and mobile elements are frequent. These genetic exchanges are also key for the rapid dissemination of antibiotic resistance. Here, we review recent studies that have greatly extended our knowledge of the mechanisms underlying horizontal gene transfer, the ecological complexities of a network of interactions involving bacteria and their mobile elements, and the effect of host physiology on the rates of genetic exchanges. Furthermore, we discuss other, fundamental challenges in detecting and quantifying genetic exchanges in vivo, and how studies have contributed to start overcoming these challenges. We highlight the importance of integrating novel computational approaches and theoretical models with experimental methods where multiple strains and transfer elements are studied, both in vivo and in controlled conditions that mimic the intricacies of host-associated environments.
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Affiliation(s)
- Jorge Moura de Sousa
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, Paris, 75015 Paris, France
| | - Marta Lourenço
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, F-75015 Paris, France
| | - Isabel Gordo
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande,6, Oeiras, Portugal.
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12
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Xu C, Rao J, Xie Y, Lu J, Li Z, Dong C, Wang L, Jiang J, Chen C, Chen S. The DNA Phosphorothioation Restriction-Modification System Influences the Antimicrobial Resistance of Pathogenic Bacteria. Microbiol Spectr 2023; 11:e0350922. [PMID: 36598279 PMCID: PMC9927239 DOI: 10.1128/spectrum.03509-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 11/30/2022] [Indexed: 01/05/2023] Open
Abstract
Bacterial defense barriers, such as DNA methylation-associated restriction-modification (R-M) and the CRISPR-Cas system, play an important role in bacterial antimicrobial resistance (AMR). Recently, a novel R-M system based on DNA phosphorothioate (PT) modification has been shown to be widespread in the kingdom of Bacteria as well as Archaea. However, the potential role of the PT R-M system in bacterial AMR remains unclear. In this study, we explored the role of PT R-Ms in AMR with a series of common clinical pathogenic bacteria. By analyzing the distribution of AMR genes related to mobile genetic elements (MGEs), it was shown that the presence of PT R-M effectively reduced the distribution of horizontal gene transfer (HGT)-derived AMR genes in the genome, even in the bacteria that did not tend to acquire AMR genes by HGT. In addition, unique gene variation analysis based on pangenome analysis and MGE prediction revealed that the presence of PT R-M could suppress HGT frequency. Thus, this is the first report showing that the PT R-M system has the potential to repress HGT-derived AMR gene acquisition by reducing the HGT frequency. IMPORTANCE In this study, we demonstrated the effect of DNA PT modification-based R-M systems on horizontal gene transfer of AMR genes in pathogenic bacteria. We show that there is no apparent association between the genetic background of the strains harboring PT R-Ms and the number of AMR genes or the kinds of gene families. The strains equipped with PT R-M harbor fewer plasmid-derived, prophage-derived, or integrating mobile genetic element (iMGE)-related AMR genes and have a lower HGT frequency, but the degree of inhibition varies among different bacteria. In addition, compared with Salmonella enterica and Escherichia coli, Klebsiella pneumoniae prefers to acquire MGE-derived AMR genes, and there is no coevolution between PT R-M clusters and bacterial core genes.
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Affiliation(s)
- Congrui Xu
- Brain Center, Department of Neurosurgery, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Jing Rao
- Brain Center, Department of Neurosurgery, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Yuqing Xie
- Brain Center, Department of Neurosurgery, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Jiajun Lu
- Information Engineering Institute, Wuchang Institute of Technology, Wuhan, China
| | - Zhiqiang Li
- Brain Center, Department of Neurosurgery, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Changjiang Dong
- Brain Center, Department of Neurosurgery, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Lianrong Wang
- Brain Center, Department of Neurosurgery, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Jinghong Jiang
- Department of Obstetrics & Gynecology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Chao Chen
- Department of Burn and Plastic Surgery, Shenzhen Institute of Translational Medicine, Health Science Center, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Shi Chen
- Brain Center, Department of Neurosurgery, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
- Department of Burn and Plastic Surgery, Shenzhen Institute of Translational Medicine, Health Science Center, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
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13
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Radovanovic M, Kekic D, Jovicevic M, Kabic J, Gajic I, Opavski N, Ranin L. Current Susceptibility Surveillance and Distribution of Antimicrobial Resistance in N. gonorrheae within WHO Regions. Pathogens 2022; 11:1230. [PMID: 36364980 PMCID: PMC9697523 DOI: 10.3390/pathogens11111230] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 10/18/2022] [Accepted: 10/21/2022] [Indexed: 08/01/2023] Open
Abstract
Neisseria gonorrhoeae (N. gonorrhoeae) is the etiological agent of the second most common sexually transmitted disease in the world, gonorrhoea. Currently recommended and last available first-line therapy is extended-spectrum cephalosporins most often combined with azitromycin. However, misuse of antibiotics and the abilities of N. gonorrhoeae to acquire new genetic and plasmid-borne resistance determinants has gradually led to the situation where this bacterium has become resistant to all major classes of antibiotics. Together with a generally slow update of treatment guidelines globally, as well as with the high capacity of gonococci to develop and retain AMR, this may lead to the global worsening of gonococcal AMR. Since effective vaccines are unavailable, the management of gonorrhoea relies mostly on prevention and accurate diagnosis, together with antimicrobial treatment. The study overviews the latest results of mostly WHO-initiated studies, primarily focusing on the data regarding the molecular basis of the resistance to the current and novel most promising antibacterial agents, which could serve to establish or reinforce the continual, quality-assured and comparable AMR surveillance, including systematic monitoring and treatment with the use of molecular AMR prediction methods.
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Affiliation(s)
- Marina Radovanovic
- Department of Biochemistry, Institute for Biological Research “Siniša Stanković”, University of Belgrade, Belgrade 11000, Serbia
| | - Dusan Kekic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade 11000, Serbia
| | - Milos Jovicevic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade 11000, Serbia
| | - Jovana Kabic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade 11000, Serbia
| | - Ina Gajic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade 11000, Serbia
| | - Natasa Opavski
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade 11000, Serbia
| | - Lazar Ranin
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade 11000, Serbia
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14
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Canary in the Coal Mine: How Resistance Surveillance in Commensals Could Help Curb the Spread of AMR in Pathogenic Neisseria. mBio 2022; 13:e0199122. [PMID: 36154280 DOI: 10.1128/mbio.01991-22] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Antimicrobial resistance (AMR) is widespread within Neisseria gonorrhoeae populations. Recent work has highlighted the importance of commensal Neisseria (cN) as a source of AMR for their pathogenic relatives through horizontal gene transfer (HGT) of AMR alleles, such as mosaic penicillin binding protein 2 (penA), multiple transferable efflux pump (mtr), and DNA gyrase subunit A (gyrA) which impact beta-lactam, azithromycin, and ciprofloxacin susceptibility, respectively. However, nonpathogenic commensal species are rarely characterized. Here, we propose that surveillance of the universally carried commensal Neisseria may play the role of the "canary in the coal mine," and reveal circulating known and novel antimicrobial resistance determinants transferable to pathogenic Neisseria. We summarize the current understanding of commensal Neisseria as an AMR reservoir, and call to increase research on commensal Neisseria species, through expanding established gonococcal surveillance programs to include the collection, isolation, antimicrobial resistance phenotyping, and whole-genome sequencing (WGS) of commensal isolates. This will help combat AMR in the pathogenic Neisseria by: (i) determining the contemporary AMR profile of commensal Neisseria, (ii) correlating AMR phenotypes with known and novel genetic determinants, (iii) qualifying and quantifying horizontal gene transfer (HGT) for AMR determinants, and (iv) expanding commensal Neisseria genomic databases, perhaps leading to the identification of new drug and vaccine targets. The proposed modification to established Neisseria collection protocols could transform our ability to address AMR N. gonorrhoeae, while requiring minor modifications to current surveillance practices. IMPORTANCE Contemporary increases in the prevalence of antimicrobial resistance (AMR) in Neisseria gonorrhoeae populations is a direct threat to global public health and the effective treatment of gonorrhea. Substantial effort and financial support are being spent on identifying resistance mechanisms circulating within the gonococcal population. However, these surveys often overlook a known source of resistance for gonococci-the commensal Neisseria. Commensal Neisseria and pathogenic Neisseria frequently share DNA through horizontal gene transfer, which has played a large role in rendering antibiotic therapies ineffective in pathogenic Neisseria populations. Here, we propose the expansion of established gonococcal surveillance programs to integrate a collection, AMR profiling, and genomic sequencing pipeline for commensal species. This proposed expansion will enhance the field's ability to identify resistance in and from nonpathogenic reservoirs and anticipate AMR trends in pathogenic Neisseria.
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15
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de Korne-Elenbaas J, Bruisten SM, van Dam AP, Maiden MCJ, Harrison OB. The Neisseria gonorrhoeae Accessory Genome and Its Association with the Core Genome and Antimicrobial Resistance. Microbiol Spectr 2022; 10:e0265421. [PMID: 35604129 PMCID: PMC9241924 DOI: 10.1128/spectrum.02654-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 04/14/2022] [Indexed: 01/22/2023] Open
Abstract
The bacterial accessory genome provides the genetic flexibility needed to facilitate environment and host adaptation. In Neisseria gonorrhoeae, known accessory elements include plasmids which can transfer and mediate antimicrobial resistance (AMR); however, chromosomal accessory genes could also play a role in AMR. Here, the gonococcal accessory genome was characterized using gene-by-gene approaches and its association with the core genome and AMR were assessed. The gonococcal accessory gene pool consisted of 247 genes, which were mainly genes located on large mobile genetic elements, phage associated genes, or genes encoding putative secretion systems. Accessory elements showed similar synteny across genomes, indicating either a predisposition for particular genomic locations or ancestral inheritance that are conserved during strain expansion. Significant associations were found between the prevalence of accessory elements and core genome multi-locus sequence types (cgMLST), consistent with a structured gonococcal population despite frequent horizontal gene transfer (HGT). Increased prevalence of putative DNA exchange regulators was significantly associated with AMR, which included a putative secretion system, methyltransferases and a toxin-antitoxin system. Although frequent HGT results in high genetic diversity in the gonococcus, we found that this is mediated by a small gene pool. In fact, a highly organized genome composition was identified with a strong association between the accessory and core genome. Increased prevalence of DNA exchange regulators in antimicrobial resistant isolates suggests that genetic material exchange plays a role in the development or maintenance of AMR. These findings enhance our understanding of gonococcal genome architecture and have important implications for gonococcal population biology. IMPORTANCE The emergence of antimicrobial resistance (AMR) against third generation cephalosporins in Neisseria gonorrhoeae is a major public health concern, as these are antibiotics of last resort for the effective treatment of gonorrhea. Although the resistance mechanisms against this class of antibiotics have not been entirely resolved, resistance against other classes of antibiotics, such as tetracyclines, is known to be mediated through plasmids, which are known gonococcal extra-chromosomal accessory elements. A complete assessment of the chromosomal accessory genome content and its role in AMR has not yet been undertaken. Here, we comprehensively characterize the gonococcal accessory genome to better understand genome architecture as well as the evolution and mechanisms of AMR in this species.
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Affiliation(s)
- Jolinda de Korne-Elenbaas
- Public Health Laboratory, Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, the Netherlands
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology, Amsterdam Institute for Infection and Immunity (AI&II), Academic Medical Center, Amsterdam, the Netherlands
| | - Sylvia M. Bruisten
- Public Health Laboratory, Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, the Netherlands
- Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity (AI&II), Amsterdam, the Netherlands
| | - Alje P. van Dam
- Public Health Laboratory, Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, the Netherlands
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology, Amsterdam Institute for Infection and Immunity (AI&II), Academic Medical Center, Amsterdam, the Netherlands
| | - Martin C. J. Maiden
- Department of Zoology, Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Odile B. Harrison
- Department of Zoology, Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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16
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Pandey SD, Biswas I. Clp ATPases differentially affect natural competence development in Streptococcus mutans. Microbiologyopen 2022; 11:e1288. [PMID: 35765180 PMCID: PMC9108599 DOI: 10.1002/mbo3.1288] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 04/27/2022] [Indexed: 11/25/2022] Open
Abstract
In naturally competent bacteria, DNA transformation through horizontal gene transfer is an evolutionary mechanism to receive extracellular DNA. Bacteria need to maintain a state of competence to accept foreign DNA, and this is an energy-driven phenomenon that is tightly controlled. In Streptococcus, competence development is a complex process that is not fully understood. In this study, we used Streptococcus mutans, an oral bacterium, to determine how cell density affects competence development. We found that in S. mutans the transformation efficiency is maximum when the transforming DNA was added at low cell density and incubated for 2.5 h before selecting for transformants. We also found that S. mutans cells remain competent until the mid-logarithmic phase, after which the competence decreases drastically. Surprisingly, we observed that individual components of Clp proteolytic complexes differentially regulate competence. If the transformation is carried out at the early growth phase, both ClpP protease and ClpX ATPase are needed for competence. In contrast, we found that both ClpC and ClpE negatively affect competence. We also found that if the transformation is carried out at the mid-logarithmic growth phase ClpX is still required for competence, but ClpP negatively affects competence. While the exact reason for this differential effect of ClpP and ClpX on transformation is currently unknown, we found that both ClpC and ClpE have a negative effect on transformation, which was not reported before.
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Affiliation(s)
- Satya D. Pandey
- Department of MicrobiologyUniversity of Kansas Medical CenterKansas CityKansasUSA
| | - Indranil Biswas
- Department of MicrobiologyUniversity of Kansas Medical CenterKansas CityKansasUSA
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17
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Nyongesa S, Chenal M, Bernet È, Coudray F, Veyrier FJ. Sequential markerless genetic manipulations of species from the Neisseria genus. Can J Microbiol 2022; 68:551-560. [PMID: 35512370 DOI: 10.1139/cjm-2022-0024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The development of simple and highly efficient strategies for genetic modifications are essential for post-genetic studies aimed at characterizing gene functions for various applications. We sought to develop a reliable system for Neisseria species that allows for both unmarked and accumulation of multiple genetic modifications in a single strain. In this work we developed and validated three-gene cassettes named RPLK and RPCC, comprising of an antibiotic resistance marker for positive selection, the phenotypic selection marker lacZ or mCherry, and the counter selection gene rpsL. These cassettes can be transformed with high efficiency across the Neisseria genus while significantly reducing the number of false positives compared to similar approaches. We exemplify the versatility and application of these systems by obtaining unmarked luminescent strains (knock-in) or mutants (knock-out) in different pathogenic and commensal species across the Neisseria genus in addition to the cumulative deletion of six loci in a single strain of Neisseria elongata.
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Affiliation(s)
- Sammy Nyongesa
- INRS, 14851, Centre Armand-Frappier Santé Biotechnologie, Quebec, Quebec, Canada;
| | - Martin Chenal
- INRS, 14851, Centre Armand-Frappier Santé Biotechnologie, Quebec, Quebec, Canada;
| | - Ève Bernet
- INRS, 14851, Centre Armand-Frappier Santé Biotechnologie, Quebec, Quebec, Canada;
| | - Florian Coudray
- INRS, 14851, Centre Armand-Frappier Santé Biotechnologie, Quebec, Quebec, Canada;
| | - Frédéric J Veyrier
- INRS, 14851, Centre Armand-Frappier Santé Biotechnologie, Quebec, Quebec, Canada;
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18
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de Block T, González N, Abdellati S, Laumen JGE, Van Dijck C, De Baetselier I, Van den Bossche D, Manoharan-Basil SS, Kenyon C. Successful Intra- but Not Inter-species Recombination of msr(D) in Neisseria subflava. Front Microbiol 2022; 13:855482. [PMID: 35432273 PMCID: PMC9007320 DOI: 10.3389/fmicb.2022.855482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 03/02/2022] [Indexed: 11/23/2022] Open
Abstract
Resistance acquisition via natural transformation is a common process in the Neisseria genus. Transformation has played an important role in the emergence of resistance to many antimicrobials in Neisseria gonorrhoeae and Neisseria meningitidis. In a previous study, we found that currently circulating isolates of Neisseria subflava had acquired an msr(D) gene that has been found to result in macrolide resistance in other bacteria but never found in Neisseria species before. To determine if this resistance mechanism is transferable among Neisseria species, we assessed if we could transform the msr(D) gene into other commensal and pathogenic Neisseria under low dose azithromycin pressure. Intraspecies recombination in commensal N. subflava was confirmed with PCR and resulted in high-level macrolide resistance. Whole-genome sequencing of these transformed strains identified the complete uptake of the msr(D) integration fragment. Sequence analysis showed that a large fragment of DNA (5 and 12 kb) was transferred through a single horizontal gene transfer event. Furthermore, uptake of the msr(D) gene had no apparent fitness cost. Interspecies transformation of msr(D) from N. subflava to N. gonorrhoeae was, however, not successful.
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Affiliation(s)
- Tessa de Block
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Natalia González
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Saïd Abdellati
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Jolein Gyonne Elise Laumen
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Christophe Van Dijck
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Irith De Baetselier
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | | | | | - Chris Kenyon
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Department of Medicine, University of Cape Town, Cape Town, South Africa
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19
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Raisman JC, Fiore MA, Tomin L, Adjei JKO, Aswad VX, Chu J, Domondon CJ, Donahue BA, Masciotti CA, McGrath CG, Melita J, Podbielski PA, Schreiner MR, Trumpore LJ, Wengert PC, Wrightstone EA, Hudson AO, Wadsworth CB. Evolutionary paths to macrolide resistance in a Neisseria commensal converge on ribosomal genes through short sequence duplications. PLoS One 2022; 17:e0262370. [PMID: 35025928 PMCID: PMC8758062 DOI: 10.1371/journal.pone.0262370] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/22/2021] [Indexed: 11/19/2022] Open
Abstract
Neisseria commensals are an indisputable source of resistance for their pathogenic relatives. However, the evolutionary paths commensal species take to reduced susceptibility in this genus have been relatively underexplored. Here, we leverage in vitro selection as a powerful screen to identify the genetic adaptations that produce azithromycin resistance (≥ 2 μg/mL) in the Neisseria commensal, N. elongata. Across multiple lineages (n = 7/16), we find mutations that reduce susceptibility to azithromycin converge on the locus encoding the 50S ribosomal L34 protein (rpmH) and the intergenic region proximal to the 30S ribosomal S3 protein (rpsC) through short tandem duplication events. Interestingly, one of the laboratory evolved mutations in rpmH is identical (7LKRTYQ12), and two nearly identical, to those recently reported to contribute to high-level azithromycin resistance in N. gonorrhoeae. Transformations into the ancestral N. elongata lineage confirmed the causality of both rpmH and rpsC mutations. Though most lineages inheriting duplications suffered in vitro fitness costs, one variant showed no growth defect, suggesting the possibility that it may be sustained in natural populations. Ultimately, studies like this will be critical for predicting commensal alleles that could rapidly disseminate into pathogen populations via allelic exchange across recombinogenic microbial genera.
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Affiliation(s)
- Jordan C. Raisman
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Michael A. Fiore
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Lucille Tomin
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Joseph K. O. Adjei
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Virginia X. Aswad
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Jonathan Chu
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Christina J. Domondon
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Ben A. Donahue
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Claudia A. Masciotti
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Connor G. McGrath
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Jo Melita
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Paul A. Podbielski
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Madelyn R. Schreiner
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Lauren J. Trumpore
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Peter C. Wengert
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Emalee A. Wrightstone
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - André O. Hudson
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Crista B. Wadsworth
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
- * E-mail:
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20
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Shaskolskiy B, Kravtsov D, Kandinov I, Gorshkova S, Kubanov A, Solomka V, Deryabin D, Dementieva E, Gryadunov D. Comparative Whole-Genome Analysis of Neisseria gonorrhoeae Isolates Revealed Changes in the Gonococcal Genetic Island and Specific Genes as a Link to Antimicrobial Resistance. Front Cell Infect Microbiol 2022; 12:831336. [PMID: 35252037 PMCID: PMC8895040 DOI: 10.3389/fcimb.2022.831336] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 01/28/2022] [Indexed: 12/24/2022] Open
Abstract
Comparative whole-genome analysis was performed for Neisseria gonorrhoeae isolates belonging to the Neisseria gonorrhoeae multiantigen sequence typing (NG-MAST) types predominant worldwide — 225, 1407, 2400, 2992, and 4186 — and to genogroup 807, the most common genogroup in the Russian Federation. Here, for the first time, the complete genomes of 25 N. gonorrhoeae isolates from genogroup 807 were obtained. For NG-MAST types 225, 1407, 2400, 2992, and 4186, genomes from the Pathogenwatch database were used. The phylogenetic network constructed for 150 genomes showed that the clustering according to NG-MAST type corresponded to the clustering according to genome. Comparisons of genomes of the six sequence types revealed 8-20 genes specific to each sequence type, including the loci for phase variations and genetic components of the gonococcal genetic island (GGI). NG-MAST type 2992 and 4186 isolates either lacked the GGI or carried critical mutations in genes essential for DNA secretion. In all analyzed genogroup 807 isolates, substitution of the essential atlA gene with the eppA gene was found, accompanied by a change in the traG allele, replacement of the ych gene with ych1, and the absence of the exp1 gene, which is likely to result in loss of GGI functionality. For the NG-MAST type 225, 1407 and 2400 isolates, no premature stop codons or reading frameshifts were found in the genes essential for GGI function. A relationship between isolate susceptibility to ciprofloxacin, penicillin, tetracycline and the presence of lesions in GGI genes necessary for DNA secretion was established. The N. gonorrhoeae evolutionary pathways, which allow a particular sequence type to maintain long-term predominance in the population, may include changes in genes responsible for adhesion and virulence, changes in the GGI structure, preservation of genes carrying drug resistance determinants, and changes in genes associated with host adaptation or encoding enzymes of biochemical pathways.
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Affiliation(s)
- Boris Shaskolskiy
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- *Correspondence: Boris Shaskolskiy,
| | - Dmitry Kravtsov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Ilya Kandinov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Sofya Gorshkova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexey Kubanov
- State Research Center of Dermatovenerology and Cosmetology, Russian Ministry of Health, Moscow, Russia
| | - Victoria Solomka
- State Research Center of Dermatovenerology and Cosmetology, Russian Ministry of Health, Moscow, Russia
| | - Dmitry Deryabin
- State Research Center of Dermatovenerology and Cosmetology, Russian Ministry of Health, Moscow, Russia
| | - Ekaterina Dementieva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry Gryadunov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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21
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Wendt KE, Walker P, Sengupta A, Ungerer J, Pakrasi HB. Engineering Natural Competence into the Fast-Growing Cyanobacterium Synechococcus elongatus Strain UTEX 2973. Appl Environ Microbiol 2022; 88:e0188221. [PMID: 34705549 PMCID: PMC8752150 DOI: 10.1128/aem.01882-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 10/25/2021] [Indexed: 11/20/2022] Open
Abstract
Natural transformation is the process by which bacteria actively take up and integrate extracellular DNA into their genomes. In cyanobacteria, natural transformation has only been experimentally demonstrated in a few species. Although cyanobacteria are important model systems for studying photosynthesis and circadian cycling, natural transformation in cyanobacteria has not been characterized to the degree that the process has been studied in other Gram-negative bacteria. Two cyanobacterial species that are 99.8% genetically identical provide a unique opportunity to better understand the nuances of natural transformation in cyanobacteria: Synechococcus elongatus PCC 7942 and Synechococcus elongatus UTEX 2973 (hereafter called Synechococcus 7942 and Synechococcus 2973, respectively). Synechococcus 7942 is a naturally transformable model system, while Synechococcus 2973 is a recently discovered species that is not naturally competent. Taking only 1.5 h to replicate, Synechococcus 2973 is the fastest-growing cyanobacterial species known and thus is a strong candidate for serving as a model organism. However, its inability to undergo natural transformation has prevented it from becoming a widely used model system. By substituting polymorphic alleles from Synechococcus 7942 for native Synechococcus 2973 alleles, natural transformation was introduced into Synechococcus 2973. Two genetic loci were found to be involved in differential natural competence between the two organisms: transformation pilus component pilN and circadian transcriptional master regulator rpaA. By using targeted genome editing and enrichment outgrowth, a strain that was both naturally transformable and fast-growing was created. This new Synechococcus 2973-T strain will serve as a valuable resource to the cyanobacterial research community. IMPORTANCE Certain bacterial species have the ability to take up naked extracellular DNA and integrate it into their genomes. This process is known as natural transformation and is widely considered to play a major role in bacterial evolution. Because of the ease of introducing new genes into naturally transformable organisms, this capacity is also highly valued in the laboratory. Cyanobacteria are photosynthetic and can therefore serve as model systems for some important aspects of plant physiology. Here, we describe the creation of a modified cyanobacterial strain (Synechococcus 2973-T) that is capable of undergoing natural transformation and has a replication time on par with that of the fastest-growing cyanobacterium discovered to date. This new cyanobacterium has the potential to serve as a new model organism for the cyanobacterial research community and will allow experiments to be completed in a fraction of the time it has taken to complete previous assays.
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Affiliation(s)
- Kristen E. Wendt
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | - Patricia Walker
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | - Annesha Sengupta
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | - Justin Ungerer
- Department of Biology, Washington University, St. Louis, Missouri, USA
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22
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Callaghan MM, Koch B, Hackett KT, Klimowicz AK, Schaub RE, Krasnogor N, Dillard JP. Expression, Localization, and Protein Interactions of the Partitioning Proteins in the Gonococcal Type IV Secretion System. Front Microbiol 2021; 12:784483. [PMID: 34975804 PMCID: PMC8716806 DOI: 10.3389/fmicb.2021.784483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/24/2021] [Indexed: 11/13/2022] Open
Abstract
Partitioning proteins are well studied as molecular organizers of chromosome and plasmid segregation during division, however little is known about the roles partitioning proteins can play within type IV secretion systems. The single-stranded DNA (ssDNA)-secreting gonococcal T4SS has two partitioning proteins, ParA and ParB. These proteins work in collaboration with the relaxase TraI as essential facilitators of type IV secretion. Bacterial two-hybrid experiments identified interactions between each partitioning protein and the relaxase. Subcellular fractionation demonstrated that ParA is found in the cellular membrane, whereas ParB is primarily in the membrane, but some of the protein is in the soluble fraction. Since TraI is known to be membrane-associated, these data suggest that the gonococcal relaxosome is a membrane-associated complex. In addition, we found that translation of ParA and ParB is controlled by an RNA switch. Different mutations within the stem-loop sequence predicted to alter folding of this RNA structure greatly increased or decreased levels of the partitioning proteins.
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Affiliation(s)
- Melanie M. Callaghan
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, United States
| | - Birgit Koch
- Interdisciplinary Computing and Complex BioSystems (ICOS), Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Kathleen T. Hackett
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, United States
| | - Amy K. Klimowicz
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, United States
| | - Ryan E. Schaub
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, United States
| | - Natalio Krasnogor
- Interdisciplinary Computing and Complex BioSystems (ICOS), Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Joseph P. Dillard
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, United States
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23
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Golparian D, Unemo M. Antimicrobial resistance prediction in Neisseria gonorrhoeae: Current status and future prospects. Expert Rev Mol Diagn 2021; 22:29-48. [PMID: 34872437 DOI: 10.1080/14737159.2022.2015329] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Several nucleic acid amplification tests (NAATs), mostly real-time PCRs, to detect antimicrobial resistance (AMR) determinants and predict AMR in Neisseria gonorrhoeae are promising, and some may be ready to apply at the point-of-care (POC), but important limitations remain with most NAATs. Next-generation sequencing (NGS) can overcome many of these limitations.Areas covered: Recent advances, with main focus on publications since 2017, in the development and use of NAATs and NGS to predict gonococcal AMR for surveillance and clinical use, and pros and cons of these tests as well as future perspectives for appropriate use of molecular AMR prediction for N. gonorrhoeae.Expert Commentary: NAATs and/or NGS for AMR prediction should supplement culture-based AMR surveillance, which will remain because it detects also AMR due to unknown AMR determinants, and translation into POC tests is imperative for the end-goal of individualized treatment, sparing ceftriaxone±azithromycin. Several challenges for direct testing of clinical, especially pharyngeal, specimens and for accurate prediction of cephalosporins and azithromycin resistance, especially using NAATs, remain. The choice of AMR prediction assay needs to carefully consider the intended use of the assay; limitations intrinsic to the AMR prediction technology, algorithms and specific to chosen methodology; specimen types analyzed; and cost-effectiveness.
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Affiliation(s)
- Daniel Golparian
- WHO Collaborating Centre for Gonorrhoea and other STIs, National Reference Laboratory for STIs, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and other STIs, National Reference Laboratory for STIs, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
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24
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Transcriptional and Translational Responsiveness of the Neisseria gonorrhoeae Type IV Secretion System to Conditions of Host Infections. Infect Immun 2021; 89:e0051921. [PMID: 34581604 DOI: 10.1128/iai.00519-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The type IV secretion system of Neisseria gonorrhoeae translocates single-stranded DNA into the extracellular space, facilitating horizontal gene transfer and initiating biofilm formation. Expression of this system has been observed to be low under laboratory conditions, and multiple levels of regulation have been identified. We used a translational fusion of lacZ to traD, the gene for the type IV secretion system coupling protein, to screen for increased type IV secretion system expression. We identified several physiologically relevant conditions, including surface adherence, decreased manganese or iron, and increased zinc or copper, which increase gonococcal type IV secretion system protein levels through transcriptional and/or translational mechanisms. These metal treatments are reminiscent of the conditions in the macrophage phagosome. The ferric uptake regulator, Fur, was found to repress traD transcript levels but to also have a second role, acting to allow TraD protein levels to increase only in the absence of iron. To better understand type IV secretion system regulation during infection, we examined transcriptomic data from active urethral infection samples from five men. The data demonstrated differential expression of 20 of 21 type IV secretion system genes during infection, indicating upregulation of genes necessary for DNA secretion during host infection.
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25
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Hua Z, Ouellette M, Makkay AM, Papke RT, Zhaxybayeva O. Nutrient supplementation experiments with saltern microbial communities implicate utilization of DNA as a source of phosphorus. THE ISME JOURNAL 2021; 15:2853-2864. [PMID: 33846564 PMCID: PMC8443641 DOI: 10.1038/s41396-021-00960-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 02/25/2021] [Accepted: 03/08/2021] [Indexed: 02/01/2023]
Abstract
All environments including hypersaline ones harbor measurable concentrations of dissolved extracellular DNA (eDNA) that can be utilized by microbes as a nutrient. However, it remains poorly understood which eDNA components are used, and who in a community utilizes it. For this study, we incubated a saltern microbial community with combinations of carbon, nitrogen, phosphorus, and DNA, and tracked the community response in each microcosm treatment via 16S rRNA and rpoB gene sequencing. We show that microbial communities used DNA only as a phosphorus source, and provision of other sources of carbon and nitrogen was needed to exhibit a substantial growth. The taxonomic composition of eDNA in the water column changed with the availability of inorganic phosphorus or supplied DNA, hinting at preferential uptake of eDNA from specific organismal sources. Especially favored for growth was eDNA from the most abundant taxa, suggesting some haloarchaea prefer eDNA from closely related taxa. The preferential eDNA consumption and differential growth under various nutrient availability regimes were associated with substantial shifts in the taxonomic composition and diversity of microcosm communities. Therefore, we conjecture that in salterns the microbial community assembly is driven by the available resources, including eDNA.
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Affiliation(s)
- Zhengshuang Hua
- grid.254880.30000 0001 2179 2404Department of Biological Sciences, Dartmouth College, Hanover, NH USA ,grid.59053.3a0000000121679639Present Address: Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, PR China
| | - Matthew Ouellette
- grid.63054.340000 0001 0860 4915Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT USA ,grid.38142.3c000000041936754XPresent Address: The Forsyth Institute, Cambridge, MA USA ,grid.38142.3c000000041936754XPresent Address: Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA USA
| | - Andrea M. Makkay
- grid.63054.340000 0001 0860 4915Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT USA
| | - R. Thane Papke
- grid.63054.340000 0001 0860 4915Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT USA
| | - Olga Zhaxybayeva
- grid.254880.30000 0001 2179 2404Department of Biological Sciences, Dartmouth College, Hanover, NH USA ,grid.254880.30000 0001 2179 2404Department of Computer Science, Dartmouth College, Hanover, NH USA
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26
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Ozma MA, Khodadadi E, Rezaee MA, Asgharzadeh M, Aghazadeh M, Zeinalzadeh E, Ganbarov K, Kafil H. Bacterial proteomics and its application for pathogenesis studies. Curr Pharm Biotechnol 2021; 23:1245-1256. [PMID: 34503411 DOI: 10.2174/1389201022666210908153234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/12/2021] [Accepted: 06/13/2021] [Indexed: 01/09/2023]
Abstract
Bacteria build their structures by implementing several macromolecules such as proteins, polysaccharides, phospholipids, and nucleic acids, which leads to preserve their lives and play an essential role in their pathogenesis. There are two genomic and proteomic methods to study various macromolecules of bacteria, which are complementary methods and provide comprehensive information. Proteomic approaches are used to identify proteins and their cell applications. Furthermore, to study bacterial proteins, macromolecules are involved in the bacteria's structures and functions. These protein-based methods provide comprehensive information about the cells, such as the external structures, internal compositions, post-translational modifications, and mechanisms of particular actions such as biofilm formation, antibiotic resistance, and adaptation to the environment, which are helpful in promoting bacterial pathogenesis. These methods use various devices such as MALDI-TOF MS, LC-MS, and two-dimensional electrophoresis, which are valuable tools for studying different structural and functional proteins of the bacteria and their mechanisms of pathogenesis that causes rapid, easy, and accurate diagnosis of the infections.
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Affiliation(s)
- Mahdi Asghari Ozma
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Ehsaneh Khodadadi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz. Iran
| | | | - Mohammad Asgharzadeh
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Mohammad Aghazadeh
- Microbiome and Health Research Center, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Elham Zeinalzadeh
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz. Iran
| | | | - Hossein Kafil
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz 5166614711. Iran
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27
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Zhang L, Huang L, Huang M, Wang M, Zhu D, Wang M, Jia R, Chen S, Zhao X, Yang Q, Wu Y, Zhang S, Huang J, Ou X, Mao S, Gao Q, Tian B, Cheng A, Liu M. Effect of Nutritional Determinants and TonB on the Natural Transformation of Riemerella anatipestifer. Front Microbiol 2021; 12:644868. [PMID: 34447355 PMCID: PMC8383284 DOI: 10.3389/fmicb.2021.644868] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 07/13/2021] [Indexed: 11/27/2022] Open
Abstract
Riemerella anatipestifer is a gram-negative bacterium that is the first naturally competent bacterium identified in the family Flavobacteriaceae. However, the determinants that influence the natural transformation and the underlying mechanism remain unknown. In this study, we evaluated the effects of various nutritional factors of the GCB medium [glucose, L-glutamine, vitamin B1, Fe (NO3)3, NaCl, phosphate, and peptone], on the natural transformation of R. anatipestifer ATCC 11845. Among the assayed nutrients, peptone and phosphate affected the natural transformation of R. anatipestifer ATCC 11845, and the transformation frequency was significantly decreased when phosphate or peptone was removed from the GCB medium. When the iron chelator 2,2′-dipyridyl (Dip) was added, the transformation frequency was decreased by approximately 100-fold and restored gradually when Fe (NO3)3 was added, suggesting that the natural transformation of R. anatipestifer ATCC 11845 requires iron. Given the importance of TonB in nutrient transportation, we further identified whether TonB is involved in the natural transformation of R. anatipestifer ATCC 11845. Mutation of tonBA or tonBB, but not tbfA, was shown to inhibit the natural transformation of R. anatipestifer ATCC 11845 in the GCB medium. In parallel, it was shown that the tonBB mutant, but not the tonBA mutant, decreased iron acquisition in the GCB medium. This result suggested that the tonBB mutant affects the natural transformation frequency due to the deficiency of iron utilization.
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Affiliation(s)
- Li Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Li Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Mi Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Mengying Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Dekang Zhu
- Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Xinxin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Juan Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Xumin Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Sai Mao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Qun Gao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Bin Tian
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
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28
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Torasso Kasem EJ, Angelov A, Werner E, Lichev A, Vanderhaeghen S, Liebl W. Identification of New Chromosomal Loci Involved in com Genes Expression and Natural Transformation in the Actinobacterial Model Organism Micrococcus luteus. Genes (Basel) 2021; 12:genes12091307. [PMID: 34573289 PMCID: PMC8467076 DOI: 10.3390/genes12091307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/18/2021] [Accepted: 08/18/2021] [Indexed: 11/16/2022] Open
Abstract
Historically, Micrococcus luteus was one of the first organisms used to study natural transformation, one of the main routes of horizontal gene transfer among prokaryotes. However, little is known about the molecular basis of competence development in M. luteus or any other representative of the phylum of high-GC Gram-positive bacteria (Actinobacteria), while this means of genetic exchange has been studied in great detail in Gram-negative and low-GC Gram-positive bacteria (Firmicutes). In order to identify new genetic elements involved in regulation of the comEA-comEC competence operon in M. luteus, we conducted random chemical mutagenesis of a reporter strain expressing lacZ under the control of the comEA-comEC promoter, followed by the screening of dysregulated mutants. Mutants with (i) upregulated com promoter under competence-repressing conditions and (ii) mutants with a repressed com promoter under competence-inducing conditions were isolated. After genotype and phenotype screening, the genomes of several mutant strains were sequenced. A selection of putative com-influencing mutations was reinserted into the genome of the M. luteus reporter strain as markerless single-nucleotide mutations to confirm their effect on com gene expression. This strategy revealed mutations affecting com gene expression at genetic loci different from previously known genes involved in natural transformation. Several of these mutations decreased transformation frequencies by several orders of magnitude, thus indicating significant roles in competence development or DNA acquisition in M. luteus. Among the identified loci, there was a new locus containing genes with similarity to genes of the tad clusters of M. luteus and other bacteria.
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Affiliation(s)
- Enzo Joaquin Torasso Kasem
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany; (E.J.T.K.); (A.A.); (E.W.); (A.L.); (S.V.)
| | - Angel Angelov
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany; (E.J.T.K.); (A.A.); (E.W.); (A.L.); (S.V.)
- Institute of Medical Microbiology and Hygiene, University Clinic Elfriede-Aulhorn-Str. 6, 72076 Tübingen, Germany
| | - Elisa Werner
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany; (E.J.T.K.); (A.A.); (E.W.); (A.L.); (S.V.)
| | - Antoni Lichev
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany; (E.J.T.K.); (A.A.); (E.W.); (A.L.); (S.V.)
| | - Sonja Vanderhaeghen
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany; (E.J.T.K.); (A.A.); (E.W.); (A.L.); (S.V.)
| | - Wolfgang Liebl
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany; (E.J.T.K.); (A.A.); (E.W.); (A.L.); (S.V.)
- Correspondence: ; Tel.: +49-81-6171-545
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29
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Hanao M, Aoki K, Ishii Y, Shimuta K, Ohnishi M, Tateda K. Molecular characterization of Neisseria gonorrhoeae isolates collected through a national surveillance programme in Japan, 2013: evidence of the emergence of a ceftriaxone-resistant strain from a ceftriaxone-susceptible lineage. J Antimicrob Chemother 2021; 76:1769-1775. [PMID: 33930160 DOI: 10.1093/jac/dkab104] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 03/10/2021] [Indexed: 01/08/2023] Open
Abstract
OBJECTIVES To investigate the spread of ceftriaxone-resistant Neisseria gonorrhoeae lineages similar to strains H041 (2009) and FC428 (2015), we characterized 55 strains collected in 2013 from hospitals across Japan. METHODS Susceptibility testing and whole-genome sequencing. RESULTS Susceptibility rates were 58% for cefixime and 98% for ceftriaxone. The 55 strains were whole-genome sequenced and classified into nine MLST-STs. MLST-ST1901 was the most prevalent (n = 19) followed by MLST-ST7363 (n = 12) and MLST-ST7359 (n = 11). The most prevalent penA [encoding penicillin binding protein 2 (PBP2)] mosaic types, based on the N. gonorrhoeae sequence typing for antimicrobial resistance (NG-STAR) scheme, were 10.001 (n = 20) followed by 34.001 (n = 13). The H041 and FC428 strains were not detected; however, a single ceftriaxone-resistant strain (TUM15748) with a MIC of 0.5 mg/L ceftriaxone was identified. The TUM15748 strain belonged to MLST-ST7359 and N. gonorrhoeae multiantigen sequence typing-ST6771, and had a novel PBP2 (PBP2TUM15748, penA type 169.001). The amino acid sequence of PBP2TUM15748 showed partial similarity to that of PBP2 from N. gonorrhoeae GU140106 and commensal Neisseria perflava and Neisseria cinerea. Natural transformation and recombination experiments using full-length TUM15748 penA showed that the ceftriaxone MICs of transformants increased 16-fold or more compared with the parental ceftriaxone-susceptible recipient strain (NG9807, belonging to MLST-ST7363). No ceftriaxone-resistant MLST-ST7359 strains have previously been reported. CONCLUSIONS We showed here that a ceftriaxone-susceptible lineage acquired a mutant PBP2 mosaic type, integrating partial PBP2 sequences from commensal Neisseria species, resulting in the emergence of ceftriaxone-resistant strains.
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Affiliation(s)
- Mami Hanao
- Department of Microbiology and Infectious Diseases, Toho University Graduate School of Medicine, Tokyo, Japan.,Department of Medical Technology, Faculty of Health Science, Tokyo University of Technology, Tokyo, Japan
| | - Kotaro Aoki
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - Yoshikazu Ishii
- Department of Microbiology and Infectious Diseases, Toho University Graduate School of Medicine, Tokyo, Japan.,Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - Ken Shimuta
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan.,Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kazuhiro Tateda
- Department of Microbiology and Infectious Diseases, Toho University Graduate School of Medicine, Tokyo, Japan.,Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
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30
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Bakkali M. A cross-species genome-wide analysis of sequences similar to those involved in DNA uptake bias in the Pastuerellaceae and Neisseriaceae families of pathogenic bacteria. Genomics 2021; 113:2800-2811. [PMID: 34157405 DOI: 10.1016/j.ygeno.2021.06.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 05/22/2021] [Accepted: 06/14/2021] [Indexed: 11/19/2022]
Abstract
Acquiring new DNA allows the emergence of drug resistance in bacteria. Some Pasteurellaceae and Neisseriaceae species preferentially take up specific sequence tags. The study of such sequences is therefore relevant. They are over-represented in the genomes of the corresponding species. I found similar sequences to be present only in, but not in all, the genomes of the Pasteurellaceae and Neisseriaceae families. The genomic densities of these sequences are different both between species and between families. Interestingly, the family whose genomes harbor more of such sequences also shows more sequence types. A phylogenetic analysis allowed inferring the possible ancestral Neisseriacean sequence and a nucleotide-by-nucleotide analysis allowed inferring the potential ancestral Pasteurellacean sequence based on its genomic footprint. The method used for this work could be applied to other sequences, including transcription factor binding and repeated DNAs.
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Affiliation(s)
- M Bakkali
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain.
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Antimicrobial Resistance Profiles of Human Commensal Neisseria Species. Antibiotics (Basel) 2021; 10:antibiotics10050538. [PMID: 34066576 PMCID: PMC8148603 DOI: 10.3390/antibiotics10050538] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 11/17/2022] Open
Abstract
Pathogenic Neisseria gonorrhoeae causes the sexually transmitted infection gonorrhea. N. gonorrhoeae has evolved high levels of antimicrobial resistance (AR) leading to therapeutic failures even in dual-therapy treatment with azithromycin and ceftriaxone. AR mechanisms can be acquired by genetic transfer from closely related species, such as naturally competent commensal Neisseria species. At present, little is known about the antimicrobial resistance profiles of commensal Neisseria. Here, we characterized the phenotypic resistance profile of four commensal Neisseria species (N. lactamica, N. cinerea, N. mucosa, and N. elongata) against 10 commonly used antibiotics, and compared their profiles to 4 N. gonorrhoeae strains, using disk diffusion and minimal inhibitory concentration assays. Overall, we observed that 3 of the 4 commensals were more resistant to several antibiotics than pathogenic N. gonorrhoeae strains. Next, we compared publicly available protein sequences of known AR genes, including penicillin-binding-protein 2 (PBP2) from commensals and N. gonorrhoeae strains. We found mutations in PBP2 known to confer resistance in N. gonorrhoeae also present in commensal Neisseria sequences. Our results suggest that commensal Neisseria have unexplored antibiotic resistance gene pools that may be exchanged with pathogenic N. gonorrhoeae, possibly impairing drug development and clinical treatment.
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Lim KYL, Mullally CA, Haese EC, Kibble EA, McCluskey NR, Mikucki EC, Thai VC, Stubbs KA, Sarkar-Tyson M, Kahler CM. Anti-Virulence Therapeutic Approaches for Neisseria gonorrhoeae. Antibiotics (Basel) 2021; 10:antibiotics10020103. [PMID: 33494538 PMCID: PMC7911339 DOI: 10.3390/antibiotics10020103] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 01/15/2023] Open
Abstract
While antimicrobial resistance (AMR) is seen in both Neisseria gonorrhoeae and Neisseria meningitidis, the former has become resistant to commonly available over-the-counter antibiotic treatments. It is imperative then to develop new therapies that combat current AMR isolates whilst also circumventing the pathways leading to the development of AMR. This review highlights the growing research interest in developing anti-virulence therapies (AVTs) which are directed towards inhibiting virulence factors to prevent infection. By targeting virulence factors that are not essential for gonococcal survival, it is hypothesized that this will impart a smaller selective pressure for the emergence of resistance in the pathogen and in the microbiome, thus avoiding AMR development to the anti-infective. This review summates the current basis of numerous anti-virulence strategies being explored for N. gonorrhoeae.
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Affiliation(s)
- Katherine Y. L. Lim
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia; (K.Y.L.L.); (C.A.M.); (E.C.H.); (E.A.K.); (N.R.M.); (E.C.M.); (V.C.T.); (M.S.-T.)
| | - Christopher A. Mullally
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia; (K.Y.L.L.); (C.A.M.); (E.C.H.); (E.A.K.); (N.R.M.); (E.C.M.); (V.C.T.); (M.S.-T.)
| | - Ethan C. Haese
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia; (K.Y.L.L.); (C.A.M.); (E.C.H.); (E.A.K.); (N.R.M.); (E.C.M.); (V.C.T.); (M.S.-T.)
| | - Emily A. Kibble
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia; (K.Y.L.L.); (C.A.M.); (E.C.H.); (E.A.K.); (N.R.M.); (E.C.M.); (V.C.T.); (M.S.-T.)
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150, Australia
| | - Nicolie R. McCluskey
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia; (K.Y.L.L.); (C.A.M.); (E.C.H.); (E.A.K.); (N.R.M.); (E.C.M.); (V.C.T.); (M.S.-T.)
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150, Australia
| | - Edward C. Mikucki
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia; (K.Y.L.L.); (C.A.M.); (E.C.H.); (E.A.K.); (N.R.M.); (E.C.M.); (V.C.T.); (M.S.-T.)
| | - Van C. Thai
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia; (K.Y.L.L.); (C.A.M.); (E.C.H.); (E.A.K.); (N.R.M.); (E.C.M.); (V.C.T.); (M.S.-T.)
| | - Keith A. Stubbs
- School of Molecular Sciences, University of Western Australia, Crawley, WA 6009, Australia;
| | - Mitali Sarkar-Tyson
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia; (K.Y.L.L.); (C.A.M.); (E.C.H.); (E.A.K.); (N.R.M.); (E.C.M.); (V.C.T.); (M.S.-T.)
| | - Charlene M. Kahler
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia; (K.Y.L.L.); (C.A.M.); (E.C.H.); (E.A.K.); (N.R.M.); (E.C.M.); (V.C.T.); (M.S.-T.)
- Correspondence:
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Samarth DP, Kwon YM. Horizontal genetic exchange of chromosomally encoded markers between Campylobacter jejuni cells. PLoS One 2020; 15:e0241058. [PMID: 33104745 PMCID: PMC7588059 DOI: 10.1371/journal.pone.0241058] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 10/07/2020] [Indexed: 11/18/2022] Open
Abstract
Many epidemiological studies provide us with the evidence of horizontal gene transfer (HGT) contributing to the bacterial genomic diversity that benefits the bacterial populations with increased ability to adapt to the dynamic environments. Campylobacter jejuni, a major cause of acute enteritis in the U.S., often linked with severe post-infection neuropathies, has been reported to exhibit a non-clonal population structure and comparatively higher strain-level genetic variation. In this study, we provide evidence of the HGT of chromosomally encoded genetic markers between C. jejuni cells in the biphasic MH medium. We used two C. jejuni NCTC-11168 mutants harbouring distinct antibiotic-resistance genes [chloramphenicol (Cm) and kanamycin (Km)] present at two different neutral genomic loci. Cultures of both marker strains were mixed together and incubated for 5 hrs, then plated on MH agar plates supplemented with both antibiotics. The recombinant cells with double antibiotic markers were generated at the frequency of 0.02811 ± 0.0035% of the parental strains. PCR assays using locus-specific primers confirmed that transfer of the antibiotic-resistance genes was through homologous recombination. Also, the addition of chicken cecal content increased the recombination efficiency approximately up to 10-fold as compared to the biphasic MH medium (control) at P < 0.05. Furthermore, treating the co-culture with DNase I decreased the available DNA, which in turn significantly reduced recombination efficiency by 99.92% (P < 0.05). We used the cell-free supernatant of 16 hrs-culture of Wild-type C. jejuni as a template for PCR and found DNA sequences from six different genomic regions were easily amplified, indicating the presence of released chromosomal DNA in the culture supernatant. Our findings suggest that HGT in C. jejuni is facilitated in the chicken gut environment contributing to in vivo genomic diversity. Additionally, C. jejuni might have an active mechanism to release its chromosomal DNA into the extracellular environment, further expediting HGT in C. jejuni populations.
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Affiliation(s)
- Deepti Pranay Samarth
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States of America
- * E-mail:
| | - Young Min Kwon
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States of America
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States of America
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Neuhaus A, Selvaraj M, Salzer R, Langer JD, Kruse K, Kirchner L, Sanders K, Daum B, Averhoff B, Gold VAM. Cryo-electron microscopy reveals two distinct type IV pili assembled by the same bacterium. Nat Commun 2020; 11:2231. [PMID: 32376942 PMCID: PMC7203116 DOI: 10.1038/s41467-020-15650-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 03/19/2020] [Indexed: 12/19/2022] Open
Abstract
Type IV pili are flexible filaments on the surface of bacteria, consisting of a helical assembly of pilin proteins. They are involved in bacterial motility (twitching), surface adhesion, biofilm formation and DNA uptake (natural transformation). Here, we use cryo-electron microscopy and mass spectrometry to show that the bacterium Thermus thermophilus produces two forms of type IV pilus ('wide' and 'narrow'), differing in structure and protein composition. Wide pili are composed of the major pilin PilA4, while narrow pili are composed of a so-far uncharacterized pilin which we name PilA5. Functional experiments indicate that PilA4 is required for natural transformation, while PilA5 is important for twitching motility.
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Affiliation(s)
- Alexander Neuhaus
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- College of Life and Environmental Sciences, Geoffrey Pope, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Muniyandi Selvaraj
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438, Frankfurt am Main, Germany
- Laboratory of Structural Biology, Helsinki Institute of Life Science, 00014 University of Helsinki, Helsinki, Finland
| | - Ralf Salzer
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt am Main, Germany
- Structural Studies Division, Medical Research Council-Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Ave, Cambridge, CB2 0QH, UK
| | - Julian D Langer
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438, Frankfurt am Main, Germany
- Proteomics, Max Planck Institute for Brain Research, Max-von-Laue Str. 4, 60438, Frankfurt am Main, Germany
| | - Kerstin Kruse
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt am Main, Germany
| | - Lennart Kirchner
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt am Main, Germany
| | - Kelly Sanders
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- College of Life and Environmental Sciences, Geoffrey Pope, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Bertram Daum
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- College of Life and Environmental Sciences, Geoffrey Pope, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Beate Averhoff
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt am Main, Germany
| | - Vicki A M Gold
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.
- College of Life and Environmental Sciences, Geoffrey Pope, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.
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Craig L, Forest KT, Maier B. Type IV pili: dynamics, biophysics and functional consequences. Nat Rev Microbiol 2020; 17:429-440. [PMID: 30988511 DOI: 10.1038/s41579-019-0195-4] [Citation(s) in RCA: 222] [Impact Index Per Article: 55.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The surfaces of many bacteria are decorated with long, exquisitely thin appendages called type IV pili (T4P), dynamic filaments that are rapidly polymerized and depolymerized from a pool of pilin subunits. Cycles of pilus extension, binding and retraction enable T4P to perform a phenomenally diverse array of functions, including twitching motility, DNA uptake and microcolony formation. On the basis of recent developments, a comprehensive understanding is emerging of the molecular architecture of the T4P machinery and the filament it builds, providing mechanistic insights into the assembly and retraction processes. Combined microbiological and biophysical approaches have revealed how T4P dynamics influence self-organization of bacteria, how bacteria respond to external stimuli to regulate T4P activity for directed movement, and the role of T4P retraction in surface sensing. In this Review, we discuss the T4P machine architecture and filament structure and present current molecular models for T4P dynamics, with a particular focus on recent insights into T4P retraction. We also discuss the functional consequences of T4P dynamics, which have important implications for bacterial lifestyle and pathogenesis.
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Affiliation(s)
- Lisa Craig
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada.
| | - Katrina T Forest
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
| | - Berenike Maier
- Institute for Biological Physics, University of Cologne, Köln, Germany.
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Dong HV, Pham LQ, Nguyen HT, Nguyen MXB, Nguyen TV, May F, Le GM, Klausner JD. Decreased Cephalosporin Susceptibility of Oropharyngeal Neisseria Species in Antibiotic-using Men Who Have Sex With Men in Hanoi, Vietnam. Clin Infect Dis 2020; 70:1169-1175. [PMID: 31049592 PMCID: PMC7319061 DOI: 10.1093/cid/ciz365] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 04/30/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Neisseria gonorrhoeae (NG) infections are a global health burden. NG resistance to cephalosporins, which is increasingly reported, is an imminent threat to public health. Many hypothesize that commensal Neisseria species are an important reservoir for genetic material conferring antimicrobial resistance in NG; however, clinical data are lacking. METHODS Men who have sex with men (MSM) in Hanoi, Vietnam, completed a questionnaire regarding antibiotic use. We collected pharyngeal specimens, cultured Neisseria species, and measured minimum inhibitory concentrations (MICs) to ciprofloxacin, cefixime, ceftriaxone, and cefpodoxime. Using MIC criteria for antimicrobial susceptibility in NG, we categorized the Neisseria species and compared mean MIC levels between different antibiotic user groups. RESULTS Of 207 participants, 38% used at least 1 antibiotic in the past 6 months; 52% without a prescription. A median of 1 Neisseria species was cultured from each participant (range, 1-4) with 10 different Neisseria species identified overall. The proportion of Neisseria with reduced susceptibility to ciprofloxacin was 93%, cefpodoxime 84%, cefixime 31%, and ceftriaxone 28%. Antibiotic use within the past month was strongly associated with Neisseria species having increased MICs to cefixime, ceftriaxone, and cefpodoxime (mean MIC ratios of 6.27, 4.11, and 7.70, respectively), compared with those who used antibiotics between 1 and 6 months prior (P < .05, all comparisons). CONCLUSIONS MSM in our study often used antibiotics without a prescription. At least 1 commensal Neisseria species colonized all men. Recent use of any antibiotics may select for oropharyngeal Neisseria species with antimicrobial resistance. The normal flora of the oropharynx may be an important source of antimicrobial resistance in Neisseria gonorrhoeae.
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Affiliation(s)
- Huan V Dong
- Charles R. Drew University of Medicine and Sciences
- Department of Medicine, David Geffen School of Medicine
| | - Loc Q Pham
- Fielding School of Public Health, University of California, Los Angeles
- Center for Research and Training on Substance Abuse–HIV, Hanoi Medical University
| | - Hoa T Nguyen
- Department of Microbiology, National Hospital for Tropical Diseases, Hanoi, Vietnam
| | - Minh X B Nguyen
- Center for Research and Training on Substance Abuse–HIV, Hanoi Medical University
- Department of Health Behavior, University of North Carolina at Chapel Hill
| | - Trung V Nguyen
- Department of Microbiology, National Hospital for Tropical Diseases, Hanoi, Vietnam
- Department of Microbiology, Hanoi Medical University, Vietnam
| | - Folasade May
- Department of Medicine, David Geffen School of Medicine
| | - Giang M Le
- Center for Research and Training on Substance Abuse–HIV, Hanoi Medical University
| | - Jeffrey D Klausner
- Department of Medicine, David Geffen School of Medicine
- Fielding School of Public Health, University of California, Los Angeles
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Lomovatskaya LA, Romanenko AS. Secretion Systems of Bacterial Phytopathogens and Mutualists (Review). APPL BIOCHEM MICRO+ 2020. [DOI: 10.1134/s0003683820020106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Golparian D, Harris SR, Sánchez-Busó L, Hoffmann S, Shafer WM, Bentley SD, Jensen JS, Unemo M. Genomic evolution of Neisseria gonorrhoeae since the preantibiotic era (1928-2013): antimicrobial use/misuse selects for resistance and drives evolution. BMC Genomics 2020; 21:116. [PMID: 32013864 PMCID: PMC6998845 DOI: 10.1186/s12864-020-6511-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 01/20/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Multidrug-resistant Neisseria gonorrhoeae strains are prevalent, threatening gonorrhoea treatment globally, and understanding of emergence, evolution, and spread of antimicrobial resistance (AMR) in gonococci remains limited. We describe the genomic evolution of gonococci and their AMR, related to the introduction of antimicrobial therapies, examining isolates from 1928 (preantibiotic era) to 2013 in Denmark. This is, to our knowledge, the oldest gonococcal collection globally. METHODS Lyophilised isolates were revived and examined using Etest (18 antimicrobials) and whole-genome sequencing (WGS). Quality-assured genome sequences were obtained for 191 viable and 40 non-viable isolates and analysed with multiple phylogenomic approaches. RESULTS Gonococcal AMR, including an accumulation of multiple AMR determinants, started to emerge particularly in the 1950s-1970s. By the twenty-first century, resistance to most antimicrobials was common. Despite that some AMR determinants affect many physiological functions and fitness, AMR determinants were mainly selected by the use/misuse of gonorrhoea therapeutic antimicrobials. Most AMR developed in strains belonging to one multidrug-resistant (MDR) clade with close to three times higher genomic mutation rate. Modern N. gonorrhoeae was inferred to have emerged in the late-1500s and its genome became increasingly conserved over time. CONCLUSIONS WGS of gonococci from 1928 to 2013 showed that no AMR determinants, except penB, were in detectable frequency before the introduction of gonorrhoea therapeutic antimicrobials. The modern gonococcus is substantially younger than previously hypothesized and has been evolving into a more clonal species, driven by the use/misuse of antimicrobials. The MDR gonococcal clade should be further investigated for early detection of strains with predispositions to develop and maintain MDR and for initiation of public health interventions.
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Affiliation(s)
- Daniel Golparian
- WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, Department of Laboratory Medicine, Microbiology, Faculty of Medicine and Health, Örebro University, SE-710 85, Örebro, Sweden
| | - Simon R Harris
- Microbiotica Ltd, Biodata Innovation Centre, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Leonor Sánchez-Busó
- Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Steen Hoffmann
- Infection Preparedness, Research Unit for Reproductive Tract Microbiology, Statens Serum Institut, Copenhagen, Denmark
| | - William M Shafer
- Department of Microbiology and Immunology and Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, USA
- Laboratories of Bacterial Pathogenesis, VA Medical Center, Decatur, GA, USA
| | - Stephen D Bentley
- Pathogen Genomics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Jörgen S Jensen
- Infection Preparedness, Research Unit for Reproductive Tract Microbiology, Statens Serum Institut, Copenhagen, Denmark
| | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, Department of Laboratory Medicine, Microbiology, Faculty of Medicine and Health, Örebro University, SE-710 85, Örebro, Sweden.
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Meningococcal Quinolone Resistance Originated from Several Commensal Neisseria Species. Antimicrob Agents Chemother 2020; 64:AAC.01494-19. [PMID: 31740556 DOI: 10.1128/aac.01494-19] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 11/11/2019] [Indexed: 02/07/2023] Open
Abstract
Quinolone resistance is increasing in Neisseria meningitidis, with its prevalence in China being high (>70%), but its origin remains unknown. The aim of this study was to investigate the donors of mutation-harboring gyrA alleles in N. meningitidis A total of 198 N. meningitidis isolates and 293 commensal Neisseria isolates were collected between 2005 and 2018 in Shanghai, China. The MICs of ciprofloxacin were determined using the agar dilution method. The resistance-associated genes gyrA and parC were sequenced for all isolates, while a few isolates were sequenced on the Illumina platform. The prevalences of quinolone resistance in the N. meningitidis and commensal Neisseria isolates were 67.7% (134/198) and 99.3% (291/293), respectively. All 134 quinolone-resistant N. meningitidis isolates possessed mutations in T91 (n = 123) and/or D95 (n = 12) of GyrA, with 7 isolates also harboring ParC mutations and exhibiting higher MICs. Phylogenetic analysis of the gyrA sequence identified six clusters. Among the 71 mutation-harboring gyrA alleles found in 221 N. meningitidis isolates and genomes (n = 221), 12 alleles (n = 103, 46.6%) were included in the N. meningitidis cluster, while 20 alleles (n = 56) were included in the N. lactamica cluster, 27 alleles (n = 49) were included in the N. cinerea cluster, and 9 alleles (n = 10) were included in the N. subflava cluster. Genomic analyses identified the exact N. lactamica donors of seven mutation-harboring gyrA alleles (gyrA92, gyrA97, gyrA98, gyrA114, gyrA116, gyrA151, and gyrA230) and the N. subflava donor isolate of gyrA171, with the sizes of the recombinant fragments ranging from 634 to 7,499 bp. Transformation of gyrA fragments from these donor strains into a meningococcal isolate increased its ciprofloxacin MIC from 0.004 μg/ml to 0.125 or 0.19 μg/ml and to 0.5 μg/ml with further transformation of an additional ParC mutation. Over half of the quinolone-resistant N. meningitidis isolates acquired resistance by horizontal gene transfer from three commensal Neisseria species. Quinolone resistance in N. meningitidis increases in a stepwise manner.
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Heilers JH, Reiners J, Heller EM, Golzer A, Smits SHJ, van der Does C. DNA processing by the MOBH family relaxase TraI encoded within the gonococcal genetic island. Nucleic Acids Res 2019; 47:8136-8153. [PMID: 31276596 PMCID: PMC6736028 DOI: 10.1093/nar/gkz577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 06/18/2019] [Accepted: 06/26/2019] [Indexed: 11/26/2022] Open
Abstract
Relaxases of the MOBH family are often found on large plasmids, genetic islands and integrative conjugative elements. Many members of this family contain an N-terminal relaxase domain (TraI_2) followed by a disordered middle part and a C-terminal domain of unknown function (TraI_2_C). The TraI_2 domain contains two putative metal-binding motifs, an HD domain motif and an alternative 3H motif. TraI, encoded within the gonococcal genetic island of Neisseria gonorrhoeae, is the prototype of the MOBH family. SAXS experiments showed that TraI_2 and TraI_2_C form globular structures separated by an extended middle domain. The TraI_2 domain cleaves oriT-ssDNA in a site-specific Mn2+ or Co2+ dependent manner. The minimal oriT encompasses 50 nucleotides, requires an inverted repeat 3′ of the nic-site and several nucleotides around nic for efficient cleavage. Surprisingly, no stable covalent relaxase-DNA intermediate was observed. Mutagenesis of conserved tyrosines showed that cleavage was abolished in the Y212A mutant, whereas the Y212F and Y212H mutants retained residual activity. The HD and the alternative 3H motifs were essential for cleavage and the HD domain residues D162 and D267 for metal ion binding. We propose that the active site binds two metal ions, one in a high-affinity and one in a low-affinity site.
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Affiliation(s)
- Jan-Hendrik Heilers
- Institute for Biology II, Microbiology, Albert Ludwig University Freiburg, 79104 Freiburg, Germany
| | - Jens Reiners
- Biochemie I, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany.,Center for Structural Studies, Heinrich Heine University, 40225 Düsseldorf, Germany
| | | | - Annika Golzer
- Institute for Biology II, Microbiology, Albert Ludwig University Freiburg, 79104 Freiburg, Germany
| | - Sander H J Smits
- Biochemie I, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany.,Center for Structural Studies, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Chris van der Does
- Institute for Biology II, Microbiology, Albert Ludwig University Freiburg, 79104 Freiburg, Germany
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Młynarczyk-Bonikowska B, Majewska A, Malejczyk M, Młynarczyk G, Majewski S. Multiresistant Neisseria gonorrhoeae: a new threat in second decade of the XXI century. Med Microbiol Immunol 2019; 209:95-108. [PMID: 31802195 PMCID: PMC7125254 DOI: 10.1007/s00430-019-00651-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 11/26/2019] [Indexed: 12/13/2022]
Abstract
Neisseria gonorrhoeae is an etiologic agent of gonorrhoea, one of the most common sexually transmitted diseases caused by bacteria. For many years, infections caused by N. gonorrhoeae were considered to be relatively easy to treat; however, resistance has emerged successively to all therapeutic agents used in treatment of the disease, e.g., penicillin, ciprofloxacin or azithromycin. Currently, the global problem is the emergence and a threat of spread of N. gonorrhoeae strains resistant to extended-spectrum cephalosporins (ESC), such as injectable ceftriaxone and oral-used cefixime. Especially, dangerous are multi-resistant strains resistant simultaneously to ESC and azithromycin. Three strains with high-level resistance to azithromycin and resistant to ESC were first time isolated in 2018. Moreover, in 2018, the first ESBL was described in N. gonorrhoeae and that makes the threat of appearing the ESBL mechanism of resistance in N. gonorrhoeae more real, even though the strain was sensitive to ceftriaxone. Molecular typing revealed that variants resistant to ESC occurred also among strains belonging to epidemic clonal complex CC1 (genogroup G1407) distinguished in NG-MAST typing system. The G1407 genogroup, in particular the ST1407 sequence type, is currently dominant in most European countries. The presence of different mechanisms of drug resistance significantly affects clinical practice and force changes in treatment regimens and introduction of new drugs.
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Affiliation(s)
- Beata Młynarczyk-Bonikowska
- Department of Diagnostics of Sexually Transmitted Diseases, Medical University of Warsaw, 82a Koszykowa Str, 02-008, Warsaw, Poland
| | - Anna Majewska
- Department of Medical Microbiology, Medical University of Warsaw, 5 Chalubinskiego Str, 02-004, Warsaw, Poland.
| | - Magdalena Malejczyk
- Department of Diagnostics of Sexually Transmitted Diseases, Medical University of Warsaw, 82a Koszykowa Str, 02-008, Warsaw, Poland
| | - Grażyna Młynarczyk
- Department of Medical Microbiology, Medical University of Warsaw, 5 Chalubinskiego Str, 02-004, Warsaw, Poland
| | - Sławomir Majewski
- Department of Dermatology and Venereology, Medical University of Warsaw, 82a Koszykowa Str, 02-008, Warsaw, Poland
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42
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Vos M, Buckling A, Kuijper B. Sexual Selection in Bacteria? Trends Microbiol 2019; 27:972-981. [PMID: 31493990 DOI: 10.1016/j.tim.2019.07.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/03/2019] [Accepted: 07/24/2019] [Indexed: 01/05/2023]
Abstract
A main mechanism of lateral gene transfer in bacteria is transformation, where cells take up free DNA from the environment which subsequently can be recombined into the genome. Bacteria are also known to actively release DNA into the environment through secretion or lysis, which could aid uptake via transformation. Various evolutionary benefits of DNA uptake and DNA release have been proposed but these have all been framed in the context of natural selection. Here, we interpret bacterial DNA uptake and release in the context of sexual selection theory, which has been central to our understanding of the bewildering diversity of traits associated with sexual reproduction in the eukaryote world but has never been applied to prokaryotes. Specifically, we explore potential scenarios where bacteria releasing DNA into the environment could compete for successful uptake by other cells, or where bacteria could selectively take up DNA to enhance their fitness. We conclude that there is potential for sexual selection to act in bacteria, and that this might in part explain the considerable diversity in transformation-related behaviours.
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Affiliation(s)
- Michiel Vos
- European Centre for Environment and Human Health, University of Exeter Medical School, University of Exeter, Penryn Campus, Penryn, TR10 9FE, UK.
| | - Angus Buckling
- Department of Biosciences, University of Exeter, Penryn Campus, Penryn, TR10 9FE, UK
| | - Bram Kuijper
- Department of Biosciences, University of Exeter, Penryn Campus, Penryn, TR10 9FE, UK
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43
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Leclerc QJ, Lindsay JA, Knight GM. Mathematical modelling to study the horizontal transfer of antimicrobial resistance genes in bacteria: current state of the field and recommendations. J R Soc Interface 2019; 16:20190260. [PMID: 31409239 DOI: 10.1098/rsif.2019.0260] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Antimicrobial resistance (AMR) is one of the greatest public health challenges we are currently facing. To develop effective interventions against this, it is essential to understand the processes behind the spread of AMR. These are partly dependent on the dynamics of horizontal transfer of resistance genes between bacteria, which can occur by conjugation (direct contact), transformation (uptake from the environment) or transduction (mediated by bacteriophages). Mathematical modelling is a powerful tool to investigate the dynamics of AMR; however, the extent of its use to study the horizontal transfer of AMR genes is currently unclear. In this systematic review, we searched for mathematical modelling studies that focused on horizontal transfer of AMR genes. We compared their aims and methods using a list of predetermined criteria and used our results to assess the current state of this research field. Of the 43 studies we identified, most focused on the transfer of single genes by conjugation in Escherichia coli in culture and its impact on the bacterial evolutionary dynamics. Our findings highlight the existence of an important research gap in the dynamics of transformation and transduction and the overall public health implications of horizontal transfer of AMR genes. To further develop this field and improve our ability to control AMR, it is essential that we clarify the structural complexity required to study the dynamics of horizontal gene transfer, which will require cooperation between microbiologists and modellers.
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Affiliation(s)
- Quentin J Leclerc
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Jodi A Lindsay
- Institute for Infection and Immunity, St George's University of London, London, UK
| | - Gwenan M Knight
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK
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44
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Wu X, Zhao Y, Sun L, Jiang M, Wang Q, Wang Q, Yang W, Wu Y. Crystal structure of CagV, the Helicobacter pylori homologue of the T4SS protein VirB8. FEBS J 2019; 286:4294-4309. [PMID: 31230405 DOI: 10.1111/febs.14971] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/13/2019] [Accepted: 06/21/2019] [Indexed: 12/15/2022]
Abstract
The VirB/D type IV secretion system (T4SS) plays an essential role in materials transport between host cells and pathogenic Helicobacter pylori and is considered the major pathogenic mediator of H. pylori-associated gastric disease. VirB8, an inner membrane protein that interacts with many other proteins, is a crucial component for secretory function. Here, we present a crystal structure of the periplasmic domain of CagV, the VirB8 counterpart in the H. pylori Cag-T4SS. The structure reveals a fold similar to that of other VirB8 members except for the absence of the α5 helix, a discontinuous β1 strand, a larger angle between the α2 and α3 helices, a more hydrophobic surface groove, but exhibits a different dimer interface. Whether the dimerization occurs in solution was proved by mutagenesis, size-exclusion chromatography and cross-linking assays. Unlike the classical dimerization mode, the interface of the CagV dimer is principally formed by several hydrogen bonds, which indicates instability of dimerization. The structure here demonstrates the difference in dimerization among VirB8 homologues and indicates the considerable compositional and functional diversity of them in T4SS. DATABASE: Coordinates and structure factors have been deposited in the Protein Data Bank under accession codes 6IQT.
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Affiliation(s)
- Xiuling Wu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Yanhe Zhao
- Departments of Cell Biology and Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lifang Sun
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China
| | - Meiqin Jiang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Qin Wang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - QianChao Wang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Wendi Yang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Science, Fujian Normal University, Fuzhou, China
| | - Yunkun Wu
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Science, Fujian Normal University, Fuzhou, China
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45
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Callaghan MM, Heilers JH, van der Does C, Dillard JP. Secretion of Chromosomal DNA by the Neisseria gonorrhoeae Type IV Secretion System. Curr Top Microbiol Immunol 2019; 413:323-345. [PMID: 29536365 PMCID: PMC5935271 DOI: 10.1007/978-3-319-75241-9_13] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Approximately 80% of Neisseria gonorrhoeae and 17.5% of Neisseria meningitidis clinical isolates carry a ~59 kb genomic island known as the gonococcal genetic island (GGI). About half of the GGI consists of genes encoding a type IV secretion system (T4SS), and most of these genes are clustered in a ~28 kb region at one end of the GGI. Two additional genes (parA and parB) are found at the other end of the island. The remainder of the GGI consists mostly of hypothetical proteins, with several being identified as DNA-binding or DNA-processing proteins. The T4SS genes show similarity to those of the F-plasmid family of conjugation systems, with similarity in gene order and a low but significant level of sequence identity for the encoded proteins. However, several GGI-encoded proteins are unique from the F-plasmid system, such as AtlA, Yag, and TraA. Interestingly, the gonococcal T4SS does not act as a conjugation system. Instead, this T4SS secretes ssDNA into the extracellular milieu, where it can serve to transform highly competent Neisseria species, thereby increasing the transfer of genetic information. Although many of the T4SS proteins are expressed at low levels, this system has been implicated in several cellular processes. The secreted ssDNA is involved in the initial stages of biofilm formation, and the presence of the T4SS enables TonB-independent intracellular survival of N. gonorrhoeae strains during infection of cervical cells. Other GGI-like T4SSs have been identified in several other α-, β-, and γ-proteobacteria, but the function of these GGI-like T4SSs is unknown. Remarkably, the presence of the GGI is related to resistance to several antibiotics. Here, we describe our current knowledge about the GGI and its unique ssDNA-secreting T4SS.
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Affiliation(s)
- Melanie M Callaghan
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, 1550 Linden Dr, Madison, WI, 53706, USA
| | - Jan-Hendrik Heilers
- Institut für Biologie II-Mikrobiologie, Albert-Ludwigs-Universität Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
| | - Chris van der Does
- Institut für Biologie II-Mikrobiologie, Albert-Ludwigs-Universität Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
| | - Joseph P Dillard
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, 1550 Linden Dr, Madison, WI, 53706, USA.
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46
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Stingl K, Koraimann G. Prokaryotic Information Games: How and When to Take up and Secrete DNA. Curr Top Microbiol Immunol 2019. [PMID: 29536355 DOI: 10.1007/978-3-319-75241-9_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Besides transduction via bacteriophages natural transformation and bacterial conjugation are the most important mechanisms driving bacterial evolution and horizontal gene spread. Conjugation systems have evolved in eubacteria and archaea. In Gram-positive and Gram-negative bacteria, cell-to-cell DNA transport is typically facilitated by a type IV secretion system (T4SS). T4SSs also mediate uptake of free DNA in Helicobacter pylori, while most transformable bacteria use a type II secretion/type IV pilus system. In this chapter, we focus on how and when bacteria "decide" that such a DNA transport apparatus is to be expressed and assembled in a cell that becomes competent. Development of DNA uptake competence and DNA transfer competence is driven by a variety of stimuli and often involves intricate regulatory networks leading to dramatic changes in gene expression patterns and bacterial physiology. In both cases, genetically homogeneous populations generate a distinct subpopulation that is competent for DNA uptake or DNA transfer or might uniformly switch into competent state. Phenotypic conversion from one state to the other can rely on bistable genetic networks that are activated stochastically with the integration of external signaling molecules. In addition, we discuss principles of DNA uptake processes in naturally transformable bacteria and intend to understand the exceptional use of a T4SS for DNA import in the gastric pathogen H. pylori. Realizing the events that trigger developmental transformation into competence within a bacterial population will eventually help to create novel and effective therapies against the transmission of antibiotic resistances among pathogens.
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Affiliation(s)
- Kerstin Stingl
- National Reference Laboratory for Campylobacter, Department Biological Safety, Federal Institute for Risk Assessment (BfR), Diedersdorfer Weg 1, 12277, Berlin, Germany.
| | - Günther Koraimann
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010, Graz, Austria.
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47
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Kenyon CR, Schwartz IS. Effects of Sexual Network Connectivity and Antimicrobial Drug Use on Antimicrobial Resistance in Neisseria gonorrhoeae. Emerg Infect Dis 2019; 24:1195-1203. [PMID: 29912682 PMCID: PMC6038757 DOI: 10.3201/eid2407.172104] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Contemporary strategies to curtail the emergence of antimicrobial resistance in Neisseria gonorrhoeae include screening for and treating asymptomatic infections in high-prevalence populations in whom antimicrobial drug–resistant infections have typically emerged. We argue that antimicrobial resistance in these groups is driven by a combination of dense sexual network connectivity and antimicrobial drug exposure (for example, through screen-and-treat strategies for asymptomatic N. gonorrhoeae infection). Sexual network connectivity sustains a high-equilibrium prevalence of N. gonorrhoeae and increases likelihood of reinfection, whereas antimicrobial drug exposure results in selection pressure for reinfecting N. gonorrhoeae strains to acquire antimicrobial resistance genes from commensal pharyngeal or rectal flora. We propose study designs to test this hypothesis.
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48
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Comment on "Effectiveness of a Group B outer membrane vesicle meningococcal vaccine in preventing hospitalization from gonorrhea in New Zealand: a retrospective cohort study, Vaccines, 2019, 1, 5; doi:10.3390/vaccines7010005". Vaccines (Basel) 2019; 7:vaccines7010031. [PMID: 30875819 PMCID: PMC6466146 DOI: 10.3390/vaccines7010031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 03/13/2019] [Indexed: 02/01/2023] Open
Abstract
Available evidence suggests MeNZB™ is not associated with a durable effect against N. gonorrhoeae.
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49
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Tan A, Li WS, Verderosa AD, Blakeway LV, D Mubaiwa T, Totsika M, Seib KL. Moraxella catarrhalis NucM is an entry nuclease involved in extracellular DNA and RNA degradation, cell competence and biofilm scaffolding. Sci Rep 2019; 9:2579. [PMID: 30796312 PMCID: PMC6384898 DOI: 10.1038/s41598-019-39374-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 01/18/2019] [Indexed: 11/10/2022] Open
Abstract
Moraxella catarrhalis is a host-adapted bacterial pathogen that causes otitis media and exacerbations of chronic obstructive pulmonary disease. This study characterises the conserved M. catarrhalis extracellular nuclease, a member of the ββα metal finger family of nucleases, that we have named NucM. NucM shares conserved sequence motifs from the ββα nuclease family, including the DRGH catalytic core and Mg2+ co-ordination site, but otherwise shares little primary sequence identity with other family members, such as the Serratia Nuc and pneumococcal EndA nucleases. NucM is secreted from the cell and digests linear and circular nucleic acid. However, it appears that a proportion of NucM is also associated with the cell membrane and acts as an entry nuclease, facilitating transformation of M. catarrhalis cells. This is the first example of a ββα nuclease in a Gram negative bacteria that acts as an entry nuclease. In addition to its role in competence, NucM affects cell aggregation and biofilm formation by M. catarrhalis, with ΔnucM mutants having increased biofilm biomass. NucM is likely to increase the ability of cells to survive and persist in vivo, increasing the virulence of M. catarrhalis and potentially affecting the behaviour of other pathogens that co-colonise the otorhinolaryngological niche.
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Affiliation(s)
- Aimee Tan
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4215, Australia
| | - Wing-Sze Li
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4215, Australia
| | - Anthony D Verderosa
- Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, 4006, Australia
| | - Luke V Blakeway
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4215, Australia
| | - Tsitsi D Mubaiwa
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4215, Australia
| | - Makrina Totsika
- Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, 4006, Australia
| | - Kate L Seib
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4215, Australia.
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50
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He H, Zhou P, Shimabuku KK, Fang X, Li S, Lee Y, Dodd MC. Degradation and Deactivation of Bacterial Antibiotic Resistance Genes during Exposure to Free Chlorine, Monochloramine, Chlorine Dioxide, Ozone, Ultraviolet Light, and Hydroxyl Radical. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:2013-2026. [PMID: 30712343 DOI: 10.1021/acs.est.8b04393] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
This work investigated degradation (measured by qPCR) and biological deactivation (measured by culture-based natural transformation) of extra- and intracellular antibiotic resistance genes (eARGs and iARGs) by free available chlorine (FAC), NH2Cl, O3, ClO2, and UV light (254 nm), and of eARGs by •OH, using a chromosomal ARG ( blt) of multidrug-resistant Bacillus subtilis 1A189. Rate constants for degradation of four 266-1017 bp amplicons adjacent to or encompassing the acfA mutation enabling blt overexpression increased in proportion to #AT+GC bps/amplicon, or in proportion to #5'-GG-3' or 5'-TT-3' doublets/amplicon, with respective values ranging from 0.59 to 2.3 (×1011 M-1 s-1) for •OH, 1.8-6.9 (×104 M-1 s-1) for O3, 3.9-9.2 (×103 M-1 s-1) for FAC, 0.35-1.2(×101 M-1 s-1) for ClO2, and 2.0-8.8 (×10-2 cm2/mJ) for UV at pH 7, and from 1.7-4.4 M-1 s-1 for NH2Cl at pH 8. For FAC, NH2Cl, O3, ClO2, and UV, ARG deactivation paralleled degradation of amplicons approximating a ∼800-1000 bp acfA-flanking sequence required for natural transformation in B. subtilis, whereas deactivation outpaced degradation for •OH. At practical disinfectant exposures, eARGs and iARGs were ≥90% degraded/deactivated by FAC, O3, and UV, but recalcitrant to NH2Cl and ClO2. iARG degradation/ deactivation always lagged cell inactivation. These findings provide a quantitative framework for evaluating ARG fate during disinfection/oxidation, and support using qPCR as a proxy for tracking ARG deactivation under carefully selected circumstances.
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Affiliation(s)
- Huan He
- Department of Civil and Environmental Engineering , University of Washington (UW) , Seattle , Washington 98195-2700 , United States
| | - Peiran Zhou
- Department of Civil and Environmental Engineering , University of Washington (UW) , Seattle , Washington 98195-2700 , United States
| | - Kyle K Shimabuku
- Department of Civil and Environmental Engineering , University of Washington (UW) , Seattle , Washington 98195-2700 , United States
| | - Xuzhi Fang
- Department of Civil and Environmental Engineering , University of Washington (UW) , Seattle , Washington 98195-2700 , United States
| | - Shu Li
- Department of Civil and Environmental Engineering , University of Washington (UW) , Seattle , Washington 98195-2700 , United States
| | - Yunho Lee
- School of Earth Sciences and Environmental Engineering , Gwangju Institute of Science and Technology (GIST) , Gwangju 61005 , Republic of Korea
| | - Michael C Dodd
- Department of Civil and Environmental Engineering , University of Washington (UW) , Seattle , Washington 98195-2700 , United States
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